Query 010092
Match_columns 518
No_of_seqs 363 out of 1790
Neff 6.1
Searched_HMMs 46136
Date Thu Mar 28 20:57:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07598 RNA polymerase sigma 100.0 6.3E-64 1.4E-68 527.8 36.0 314 195-517 54-411 (415)
2 PRK07406 RNA polymerase sigma 100.0 6.1E-60 1.3E-64 494.1 35.9 311 199-518 61-373 (373)
3 PRK05949 RNA polymerase sigma 100.0 1.1E-59 2.3E-64 486.2 36.0 309 198-517 15-325 (327)
4 TIGR02997 Sig70-cyanoRpoD RNA 100.0 3.1E-58 6.7E-63 469.9 34.9 296 201-505 1-298 (298)
5 PRK07405 RNA polymerase sigma 100.0 6.1E-58 1.3E-62 471.5 35.9 309 198-517 5-315 (317)
6 COG0568 RpoD DNA-directed RNA 100.0 2.1E-58 4.5E-63 472.3 29.5 314 197-518 5-342 (342)
7 PRK05901 RNA polymerase sigma 100.0 1E-57 2.2E-62 491.3 31.5 303 195-518 205-509 (509)
8 PRK07921 RNA polymerase sigma 100.0 5.2E-56 1.1E-60 457.9 32.3 299 198-517 23-323 (324)
9 PRK09210 RNA polymerase sigma 100.0 7.4E-54 1.6E-58 449.3 31.2 273 197-517 92-366 (367)
10 PRK05658 RNA polymerase sigma 100.0 1.6E-50 3.4E-55 449.8 28.9 242 268-517 371-617 (619)
11 TIGR02393 RpoD_Cterm RNA polym 100.0 1.2E-46 2.5E-51 372.6 25.5 235 275-517 1-237 (238)
12 PRK05657 RNA polymerase sigma 100.0 5.3E-44 1.2E-48 369.2 29.4 270 197-514 49-320 (325)
13 PRK07500 rpoH2 RNA polymerase 100.0 1.8E-43 3.8E-48 360.0 29.5 267 198-509 3-278 (289)
14 PRK06596 RNA polymerase factor 100.0 1.7E-43 3.8E-48 359.2 29.1 261 199-509 12-281 (284)
15 TIGR02392 rpoH_proteo alternat 100.0 1.9E-42 4E-47 349.1 28.7 257 202-508 2-268 (270)
16 PRK07122 RNA polymerase sigma 100.0 1.2E-42 2.7E-47 349.5 25.8 221 273-507 39-262 (264)
17 TIGR02394 rpoS_proteo RNA poly 100.0 3.5E-40 7.6E-45 334.8 29.6 267 198-512 10-278 (285)
18 PRK07408 RNA polymerase sigma 100.0 3.8E-40 8.2E-45 330.0 27.0 227 269-509 20-252 (256)
19 TIGR02850 spore_sigG RNA polym 100.0 5.8E-39 1.3E-43 320.7 28.5 241 210-507 10-253 (254)
20 PRK05911 RNA polymerase sigma 100.0 2.7E-39 5.8E-44 324.0 24.9 228 270-508 19-253 (257)
21 COG1191 FliA DNA-directed RNA 100.0 3.9E-38 8.4E-43 312.0 24.5 226 267-509 17-245 (247)
22 PRK08215 sporulation sigma fac 100.0 1.9E-37 4.2E-42 310.3 27.4 222 269-507 32-256 (258)
23 PRK06288 RNA polymerase sigma 100.0 3.5E-36 7.6E-41 302.9 27.1 249 211-509 7-261 (268)
24 TIGR02885 spore_sigF RNA polym 100.0 3.9E-36 8.5E-41 295.6 26.0 224 267-507 4-230 (231)
25 TIGR02941 Sigma_B RNA polymera 100.0 3E-35 6.4E-40 293.8 27.5 225 271-508 26-253 (255)
26 TIGR02980 SigBFG RNA polymeras 100.0 7.2E-35 1.6E-39 285.7 25.0 222 272-507 1-225 (227)
27 PRK07670 RNA polymerase sigma 100.0 6.9E-34 1.5E-38 283.6 26.3 229 269-508 17-249 (251)
28 PRK05572 sporulation sigma fac 100.0 1.2E-33 2.7E-38 281.9 27.5 221 269-508 27-250 (252)
29 PRK12427 flagellar biosynthesi 100.0 1.2E-33 2.6E-38 279.1 25.4 213 274-506 15-229 (231)
30 TIGR02479 FliA_WhiG RNA polyme 100.0 1E-33 2.3E-38 277.3 24.4 218 279-507 1-222 (224)
31 PRK08583 RNA polymerase sigma 100.0 4.1E-33 8.8E-38 278.7 26.9 227 270-509 25-254 (257)
32 PRK06986 fliA flagellar biosyn 100.0 1.6E-32 3.4E-37 271.2 24.4 226 271-508 5-232 (236)
33 PRK05803 sporulation sigma fac 100.0 1.1E-26 2.5E-31 229.1 23.3 208 202-510 17-229 (233)
34 PRK08301 sporulation sigma fac 99.9 4.4E-23 9.6E-28 203.3 22.9 182 266-508 44-230 (234)
35 TIGR02846 spore_sigmaK RNA pol 99.9 5E-23 1.1E-27 202.6 23.1 183 267-507 41-225 (227)
36 TIGR02835 spore_sigmaE RNA pol 99.9 8.8E-22 1.9E-26 194.6 22.3 184 265-508 43-230 (234)
37 PRK08295 RNA polymerase factor 99.9 8.3E-21 1.8E-25 182.8 19.8 187 264-510 14-204 (208)
38 PRK09648 RNA polymerase sigma 99.9 2.9E-20 6.4E-25 176.9 20.1 171 265-508 15-187 (189)
39 TIGR02859 spore_sigH RNA polym 99.9 3E-20 6.5E-25 177.4 19.1 185 263-507 8-196 (198)
40 PRK12513 RNA polymerase sigma 99.9 1.6E-20 3.6E-25 179.4 17.2 177 262-512 14-191 (194)
41 PRK09652 RNA polymerase sigma 99.9 2.1E-20 4.5E-25 174.8 17.4 174 267-509 3-177 (182)
42 PRK05602 RNA polymerase sigma 99.9 3E-20 6.5E-25 176.4 18.0 169 264-510 10-178 (186)
43 PRK09646 RNA polymerase sigma 99.8 4.6E-20 1E-24 176.7 18.6 170 265-509 21-191 (194)
44 TIGR02952 Sig70_famx2 RNA poly 99.8 6.6E-20 1.4E-24 170.5 18.8 167 266-507 3-169 (170)
45 TIGR02948 SigW_bacill RNA poly 99.8 5.5E-20 1.2E-24 173.8 17.7 177 263-508 7-184 (187)
46 PRK06759 RNA polymerase factor 99.8 6.5E-20 1.4E-24 168.2 16.8 152 272-507 2-153 (154)
47 PRK09641 RNA polymerase sigma 99.8 1.6E-19 3.4E-24 170.7 19.0 176 264-508 8-184 (187)
48 PRK11922 RNA polymerase sigma 99.8 1.2E-19 2.6E-24 178.9 18.8 175 268-510 24-199 (231)
49 PRK06811 RNA polymerase factor 99.8 1.7E-19 3.6E-24 172.2 18.4 175 263-511 7-182 (189)
50 PRK13919 putative RNA polymera 99.8 2.3E-19 5E-24 170.0 18.0 171 264-508 13-183 (186)
51 PRK12519 RNA polymerase sigma 99.8 2.2E-19 4.8E-24 171.4 17.9 171 264-508 19-189 (194)
52 TIGR02939 RpoE_Sigma70 RNA pol 99.8 5.3E-19 1.1E-23 167.5 19.1 177 264-509 10-187 (190)
53 PRK12514 RNA polymerase sigma 99.8 4.2E-19 9.2E-24 167.4 18.1 168 265-508 10-177 (179)
54 PRK12524 RNA polymerase sigma 99.8 4.7E-19 1E-23 170.0 18.1 171 263-509 15-185 (196)
55 PRK11923 algU RNA polymerase s 99.8 7.3E-19 1.6E-23 167.7 19.1 177 264-509 10-187 (193)
56 PRK11924 RNA polymerase sigma 99.8 7.7E-19 1.7E-23 163.8 18.8 170 266-510 5-175 (179)
57 PRK09640 RNA polymerase sigma 99.8 3.5E-19 7.5E-24 169.7 16.4 160 271-508 23-182 (188)
58 PRK12537 RNA polymerase sigma 99.8 5.6E-19 1.2E-23 167.5 17.3 168 264-508 13-181 (182)
59 PRK12534 RNA polymerase sigma 99.8 6E-19 1.3E-23 167.5 16.9 170 265-508 16-185 (187)
60 PRK12538 RNA polymerase sigma 99.8 8.2E-19 1.8E-23 173.7 18.1 169 263-509 52-220 (233)
61 PRK12531 RNA polymerase sigma 99.8 9.4E-19 2E-23 167.7 18.0 175 265-512 18-193 (194)
62 PRK12515 RNA polymerase sigma 99.8 9.8E-19 2.1E-23 166.6 17.5 173 263-512 11-183 (189)
63 TIGR02937 sigma70-ECF RNA poly 99.8 1.6E-18 3.4E-23 155.5 17.3 155 275-507 2-157 (158)
64 PRK12542 RNA polymerase sigma 99.8 4.1E-19 9E-24 168.6 14.1 171 269-512 4-174 (185)
65 TIGR02984 Sig-70_plancto1 RNA 99.8 1.5E-18 3.3E-23 164.0 17.8 182 270-507 3-187 (189)
66 PRK12526 RNA polymerase sigma 99.8 1.9E-18 4.2E-23 167.4 17.8 173 265-509 29-202 (206)
67 TIGR02895 spore_sigI RNA polym 99.8 3.6E-18 7.9E-23 167.5 19.4 186 267-498 3-198 (218)
68 TIGR02985 Sig70_bacteroi1 RNA 99.8 4.6E-18 1E-22 155.6 18.5 160 274-507 1-160 (161)
69 PRK12543 RNA polymerase sigma 99.8 4E-18 8.6E-23 161.2 17.4 165 270-510 3-167 (179)
70 PRK09643 RNA polymerase sigma 99.8 6E-18 1.3E-22 162.1 18.5 167 263-509 16-183 (192)
71 PRK12536 RNA polymerase sigma 99.8 5E-18 1.1E-22 160.8 17.8 168 264-510 11-179 (181)
72 PRK12512 RNA polymerase sigma 99.8 7.6E-18 1.7E-22 159.5 18.7 167 265-510 13-181 (184)
73 PRK09638 RNA polymerase sigma 99.8 3.5E-18 7.5E-23 160.4 15.9 167 264-508 8-174 (176)
74 PRK12522 RNA polymerase sigma 99.8 9.4E-18 2E-22 157.5 17.5 164 274-508 3-167 (173)
75 PRK09415 RNA polymerase factor 99.8 9.1E-18 2E-22 158.9 17.5 163 270-508 12-175 (179)
76 TIGR02954 Sig70_famx3 RNA poly 99.8 9.9E-18 2.2E-22 156.6 17.5 162 264-508 6-167 (169)
77 PRK12539 RNA polymerase sigma 99.8 1.5E-17 3.3E-22 157.9 18.5 168 265-509 12-180 (184)
78 PRK09645 RNA polymerase sigma 99.8 1.2E-17 2.6E-22 156.5 17.3 163 270-509 5-167 (173)
79 PRK09649 RNA polymerase sigma 99.8 1E-17 2.2E-22 159.7 16.9 168 265-513 15-183 (185)
80 TIGR02989 Sig-70_gvs1 RNA poly 99.8 1.3E-17 2.8E-22 153.6 16.8 157 274-507 1-158 (159)
81 TIGR03001 Sig-70_gmx1 RNA poly 99.8 1.4E-17 3.1E-22 166.1 18.3 178 263-516 28-217 (244)
82 PRK12518 RNA polymerase sigma 99.8 1E-17 2.2E-22 157.0 15.7 168 266-510 3-170 (175)
83 TIGR02999 Sig-70_X6 RNA polyme 99.8 1.9E-17 4.1E-22 156.3 17.1 167 265-507 8-181 (183)
84 PRK12520 RNA polymerase sigma 99.8 1.8E-17 4E-22 158.1 17.1 180 275-512 3-183 (191)
85 COG1595 RpoE DNA-directed RNA 99.7 6.9E-17 1.5E-21 153.3 18.9 170 265-509 6-176 (182)
86 PRK09647 RNA polymerase sigma 99.7 4.7E-17 1E-21 157.8 18.1 164 270-509 24-187 (203)
87 PRK12529 RNA polymerase sigma 99.7 5.5E-17 1.2E-21 153.5 18.1 166 268-507 7-174 (178)
88 PRK12533 RNA polymerase sigma 99.7 6.1E-17 1.3E-21 158.7 18.6 169 270-509 14-183 (216)
89 TIGR02983 SigE-fam_strep RNA p 99.7 5.7E-17 1.2E-21 150.2 16.2 157 270-508 2-158 (162)
90 PRK12523 RNA polymerase sigma 99.7 9.5E-17 2.1E-21 150.7 17.5 164 269-509 5-168 (172)
91 PRK12516 RNA polymerase sigma 99.7 8.1E-17 1.8E-21 154.0 17.0 160 271-510 7-166 (187)
92 TIGR02947 SigH_actino RNA poly 99.7 4.6E-17 1E-21 155.6 15.1 173 270-509 7-180 (193)
93 PRK12528 RNA polymerase sigma 99.7 2.7E-16 5.9E-21 145.8 18.9 158 273-507 3-160 (161)
94 PRK09642 RNA polymerase sigma 99.7 6E-17 1.3E-21 149.8 14.3 154 281-510 2-156 (160)
95 PRK12535 RNA polymerase sigma 99.7 2.1E-16 4.5E-21 152.3 17.9 167 264-509 15-182 (196)
96 PRK12541 RNA polymerase sigma 99.7 2E-16 4.4E-21 146.6 17.2 158 271-507 2-159 (161)
97 PRK09639 RNA polymerase sigma 99.7 2.2E-16 4.8E-21 146.6 16.9 158 273-509 2-160 (166)
98 TIGR02960 SigX5 RNA polymerase 99.7 2.9E-16 6.4E-21 161.5 18.8 182 271-509 2-191 (324)
99 PRK08241 RNA polymerase factor 99.7 3E-16 6.6E-21 162.8 19.0 188 263-507 8-200 (339)
100 PRK09644 RNA polymerase sigma 99.7 2.1E-16 4.6E-21 147.2 16.0 155 276-510 3-158 (165)
101 PRK12547 RNA polymerase sigma 99.7 3E-16 6.5E-21 146.4 16.9 156 273-509 5-161 (164)
102 PRK12532 RNA polymerase sigma 99.7 2.9E-16 6.4E-21 150.3 16.5 180 277-513 8-189 (195)
103 PRK12545 RNA polymerase sigma 99.7 3.9E-16 8.4E-21 150.8 16.9 177 279-511 13-190 (201)
104 TIGR02943 Sig70_famx1 RNA poly 99.7 4.5E-16 9.8E-21 148.8 17.0 178 277-512 5-183 (188)
105 PRK12530 RNA polymerase sigma 99.7 4.5E-16 9.7E-21 148.8 17.0 174 277-510 10-184 (189)
106 PRK12544 RNA polymerase sigma 99.7 6.2E-16 1.3E-20 150.3 16.8 181 276-513 20-201 (206)
107 TIGR02950 SigM_subfam RNA poly 99.7 2.5E-16 5.4E-21 144.3 12.4 150 281-507 2-152 (154)
108 PRK09637 RNA polymerase sigma 99.7 1.2E-15 2.7E-20 145.0 17.3 152 276-509 3-155 (181)
109 PRK12540 RNA polymerase sigma 99.7 1.4E-15 3.1E-20 144.8 16.7 158 274-512 5-163 (182)
110 PRK07037 extracytoplasmic-func 99.7 1.5E-15 3.3E-20 140.8 16.1 156 278-509 2-158 (163)
111 PRK12517 RNA polymerase sigma 99.7 2.1E-15 4.6E-20 144.2 17.1 162 268-510 17-178 (188)
112 PRK09651 RNA polymerase sigma 99.7 4.4E-15 9.6E-20 139.7 18.7 160 271-507 7-166 (172)
113 TIGR02959 SigZ RNA polymerase 99.7 1.7E-15 3.6E-20 142.4 15.7 147 281-509 2-149 (170)
114 PRK12527 RNA polymerase sigma 99.7 1.4E-15 3.1E-20 140.6 15.0 153 281-509 2-154 (159)
115 PRK12546 RNA polymerase sigma 99.6 4.1E-15 8.9E-20 142.5 16.9 157 273-510 7-163 (188)
116 PRK12525 RNA polymerase sigma 99.6 1.5E-14 3.3E-19 135.4 18.8 159 273-508 8-166 (168)
117 PRK12511 RNA polymerase sigma 99.6 9.3E-15 2E-19 139.3 16.3 154 276-509 6-160 (182)
118 PRK09636 RNA polymerase sigma 99.6 1.4E-14 3.1E-19 147.8 16.1 159 274-508 4-163 (293)
119 PRK09047 RNA polymerase factor 99.6 1.5E-14 3.3E-19 133.4 13.9 152 299-510 2-156 (161)
120 PRK06704 RNA polymerase factor 99.6 6.1E-14 1.3E-18 138.7 15.4 158 264-509 8-165 (228)
121 TIGR02957 SigX4 RNA polymerase 99.5 1.1E-13 2.5E-18 140.5 16.3 155 278-508 1-156 (281)
122 PRK09635 sigI RNA polymerase s 99.5 1.6E-13 3.4E-18 140.4 16.2 160 274-507 5-165 (290)
123 PRK09191 two-component respons 99.4 1.6E-12 3.5E-17 128.3 13.9 136 275-509 2-137 (261)
124 PRK08311 putative RNA polymera 99.4 1.6E-11 3.5E-16 122.2 19.8 80 265-347 9-90 (237)
125 TIGR03209 P21_Cbot clostridium 99.4 6.9E-12 1.5E-16 114.0 13.7 136 276-494 1-141 (142)
126 PF07638 Sigma70_ECF: ECF sigm 99.3 6E-11 1.3E-15 113.5 16.4 175 263-508 6-183 (185)
127 PF04545 Sigma70_r4: Sigma-70, 99.2 4.1E-11 8.9E-16 90.6 6.2 50 453-506 1-50 (50)
128 PF04542 Sigma70_r2: Sigma-70 99.1 1.9E-10 4.1E-15 91.6 7.7 66 279-347 1-66 (71)
129 PF04539 Sigma70_r3: Sigma-70 98.9 2.3E-09 4.9E-14 88.2 7.0 75 366-440 2-77 (78)
130 PF08281 Sigma70_r4_2: Sigma-7 98.9 5.6E-09 1.2E-13 79.9 7.3 54 447-504 1-54 (54)
131 PRK06930 positive control sigm 98.5 4.7E-07 1E-11 86.0 8.4 66 440-509 98-163 (170)
132 cd06171 Sigma70_r4 Sigma70, re 98.3 3.4E-06 7.4E-11 62.5 7.1 54 448-505 2-55 (55)
133 PRK00118 putative DNA-binding 98.2 5E-06 1.1E-10 72.8 7.6 59 448-510 9-67 (104)
134 TIGR00721 tfx DNA-binding prot 98.1 4.3E-06 9.4E-11 76.6 6.6 55 456-515 6-60 (137)
135 PRK03975 tfx putative transcri 98.0 7.9E-06 1.7E-10 75.3 6.1 50 455-509 5-54 (141)
136 PF04297 UPF0122: Putative hel 98.0 3.2E-05 7E-10 67.2 8.2 55 449-507 9-64 (101)
137 PRK04217 hypothetical protein; 97.9 1.4E-05 3.1E-10 70.6 5.3 55 455-513 41-95 (110)
138 smart00421 HTH_LUXR helix_turn 97.9 4E-05 8.8E-10 57.7 6.4 50 455-509 2-51 (58)
139 TIGR01636 phage_rinA phage tra 97.8 6.3E-05 1.4E-09 68.7 7.7 61 445-507 71-131 (134)
140 PF00140 Sigma70_r1_2: Sigma-7 97.7 1.3E-05 2.8E-10 57.2 1.3 33 200-232 1-33 (37)
141 cd06170 LuxR_C_like C-terminal 97.7 0.00014 3.1E-09 54.9 7.1 49 457-510 1-49 (57)
142 PF00196 GerE: Bacterial regul 97.7 0.00012 2.6E-09 56.9 6.4 52 455-511 2-53 (58)
143 PF07374 DUF1492: Protein of u 97.7 0.00018 4E-09 62.4 7.9 56 445-504 43-99 (100)
144 PF04967 HTH_10: HTH DNA bindi 97.6 0.00027 5.8E-09 54.5 6.7 48 457-504 1-51 (53)
145 TIGR01321 TrpR trp operon repr 97.6 9.7E-05 2.1E-09 63.4 4.8 51 448-498 23-77 (94)
146 TIGR03879 near_KaiC_dom probab 97.5 0.00023 5E-09 58.4 5.6 48 449-499 8-55 (73)
147 PRK15201 fimbriae regulatory p 97.3 0.00058 1.3E-08 65.0 6.9 51 456-511 133-183 (198)
148 PRK15411 rcsA colanic acid cap 97.3 0.00043 9.4E-09 67.5 6.2 50 456-510 137-186 (207)
149 PRK10840 transcriptional regul 97.2 0.00052 1.1E-08 66.2 6.1 52 455-511 149-200 (216)
150 PRK11475 DNA-binding transcrip 97.2 0.00052 1.1E-08 67.1 6.0 52 455-511 133-184 (207)
151 TIGR03541 reg_near_HchA LuxR f 97.2 0.00066 1.4E-08 67.4 6.9 54 454-512 169-222 (232)
152 TIGR03020 EpsA transcriptional 97.2 0.00063 1.4E-08 68.5 6.7 54 454-512 188-241 (247)
153 PRK13719 conjugal transfer tra 97.2 0.00077 1.7E-08 66.2 6.8 56 451-511 138-193 (217)
154 PRK10100 DNA-binding transcrip 97.2 0.00076 1.7E-08 66.4 6.6 52 455-511 154-205 (216)
155 COG4566 TtrR Response regulato 97.1 0.002 4.3E-08 62.0 8.1 67 444-515 130-196 (202)
156 PRK13870 transcriptional regul 97.1 0.001 2.2E-08 66.3 6.1 52 456-512 173-224 (234)
157 COG2771 CsgD DNA-binding HTH d 97.0 0.0025 5.3E-08 49.6 7.1 54 455-513 3-56 (65)
158 PF13936 HTH_38: Helix-turn-he 97.0 0.00085 1.8E-08 49.6 4.1 41 455-499 3-43 (44)
159 COG2197 CitB Response regulato 97.0 0.0015 3.2E-08 64.0 6.6 53 455-512 147-199 (211)
160 PRK10188 DNA-binding transcrip 97.0 0.0016 3.5E-08 65.1 6.8 52 456-512 179-230 (240)
161 PRK09483 response regulator; P 96.8 0.0021 4.5E-08 60.9 6.0 51 455-510 147-197 (217)
162 COG3413 Predicted DNA binding 96.8 0.0028 6.1E-08 62.2 6.7 51 456-506 155-208 (215)
163 COG2739 Uncharacterized protei 96.7 0.005 1.1E-07 53.3 6.8 47 456-506 17-63 (105)
164 PRK05658 RNA polymerase sigma 96.7 0.0035 7.7E-08 70.9 7.8 38 195-232 98-135 (619)
165 PRK01381 Trp operon repressor; 96.7 0.0014 3.1E-08 56.7 3.3 50 446-495 21-74 (99)
166 PF02001 DUF134: Protein of un 96.7 0.0033 7.2E-08 55.2 5.6 49 456-508 41-89 (106)
167 PRK09390 fixJ response regulat 96.6 0.0073 1.6E-07 55.5 7.9 59 449-512 134-192 (202)
168 PRK15369 two component system 96.5 0.0069 1.5E-07 56.0 7.1 51 455-510 148-198 (211)
169 PRK10651 transcriptional regul 96.5 0.0061 1.3E-07 57.0 6.6 52 455-511 154-205 (216)
170 TIGR01637 phage_arpU phage tra 96.4 0.016 3.4E-07 52.5 8.6 60 446-507 68-128 (132)
171 COG1356 tfx Transcriptional re 96.4 0.0023 4.9E-08 57.4 2.6 50 456-510 8-57 (143)
172 PF12645 HTH_16: Helix-turn-he 96.1 0.02 4.4E-07 46.0 6.6 60 264-323 3-65 (65)
173 PRK10403 transcriptional regul 96.0 0.015 3.3E-07 54.2 6.6 54 455-513 152-205 (215)
174 PRK10360 DNA-binding transcrip 96.0 0.021 4.5E-07 53.1 7.1 57 455-516 136-192 (196)
175 PRK15320 transcriptional activ 95.9 0.014 3.1E-07 56.6 5.8 51 452-507 160-210 (251)
176 COG1342 Predicted DNA-binding 95.5 0.026 5.6E-07 48.5 5.2 48 456-507 33-80 (99)
177 PF05263 DUF722: Protein of un 95.4 0.058 1.3E-06 49.2 7.4 58 446-505 71-128 (130)
178 PRK09935 transcriptional regul 95.3 0.039 8.5E-07 51.5 6.4 49 456-509 149-197 (210)
179 TIGR02531 yecD_yerC TrpR-relat 95.2 0.042 9.1E-07 46.8 5.5 39 455-500 35-73 (88)
180 PRK13558 bacterio-opsin activa 95.2 0.035 7.6E-07 62.8 6.6 52 454-505 605-659 (665)
181 PRK09958 DNA-binding transcrip 95.2 0.047 1E-06 51.0 6.4 50 455-509 142-191 (204)
182 PF13613 HTH_Tnp_4: Helix-turn 95.1 0.046 1E-06 41.8 5.1 48 456-506 2-49 (53)
183 PF04539 Sigma70_r3: Sigma-70 95.1 0.046 1E-06 44.6 5.4 39 231-269 3-41 (78)
184 PRK04841 transcriptional regul 95.1 0.042 9.1E-07 64.1 7.1 53 455-512 837-889 (903)
185 PF13384 HTH_23: Homeodomain-l 95.0 0.022 4.8E-07 42.5 2.9 33 463-500 9-41 (50)
186 COG4941 Predicted RNA polymera 95.0 0.59 1.3E-05 49.0 14.0 57 446-506 110-166 (415)
187 PRK09210 RNA polymerase sigma 94.7 0.28 6.2E-06 52.2 11.5 129 233-406 217-347 (367)
188 PF02796 HTH_7: Helix-turn-hel 94.4 0.066 1.4E-06 39.6 4.2 33 461-498 11-43 (45)
189 PF13412 HTH_24: Winged helix- 94.4 0.11 2.3E-06 38.5 5.4 41 457-500 1-41 (48)
190 PF00325 Crp: Bacterial regula 94.0 0.058 1.3E-06 37.4 2.8 26 476-505 2-27 (32)
191 PRK07921 RNA polymerase sigma 93.9 0.7 1.5E-05 48.5 12.1 36 233-268 174-209 (324)
192 PRK15418 transcriptional regul 93.8 0.084 1.8E-06 55.1 5.0 36 463-502 20-55 (318)
193 PRK05901 RNA polymerase sigma 93.8 0.73 1.6E-05 51.2 12.5 36 233-268 359-394 (509)
194 cd00569 HTH_Hin_like Helix-tur 93.7 0.13 2.8E-06 33.9 4.2 36 457-496 6-41 (42)
195 PF01726 LexA_DNA_bind: LexA D 93.3 0.11 2.5E-06 41.6 3.9 46 454-499 1-49 (65)
196 TIGR02393 RpoD_Cterm RNA polym 93.3 0.94 2E-05 44.9 11.3 36 233-268 88-123 (238)
197 PRK07598 RNA polymerase sigma 92.4 0.94 2E-05 49.1 10.6 39 367-405 110-148 (415)
198 PF13518 HTH_28: Helix-turn-he 92.4 0.28 6E-06 36.5 4.8 27 475-501 11-37 (52)
199 PF09862 DUF2089: Protein of u 92.3 0.32 7E-06 43.3 5.8 50 453-506 30-79 (113)
200 PF06530 Phage_antitermQ: Phag 92.1 0.7 1.5E-05 41.8 7.8 50 454-507 60-109 (125)
201 PF13404 HTH_AsnC-type: AsnC-t 92.1 0.4 8.6E-06 35.1 5.1 39 458-499 2-40 (42)
202 COG1191 FliA DNA-directed RNA 92.1 2.4 5.2E-05 42.9 12.4 38 232-269 110-147 (247)
203 PF06056 Terminase_5: Putative 92.0 0.3 6.5E-06 38.4 4.7 26 475-500 12-37 (58)
204 PF10668 Phage_terminase: Phag 92.0 0.25 5.3E-06 39.2 4.2 26 474-499 20-45 (60)
205 PF04218 CENP-B_N: CENP-B N-te 91.8 0.17 3.7E-06 38.9 3.0 40 456-499 6-45 (53)
206 PF13730 HTH_36: Helix-turn-he 91.6 0.56 1.2E-05 35.5 5.7 46 456-505 2-50 (55)
207 PRK10430 DNA-binding transcrip 91.5 0.36 7.9E-06 47.3 5.8 47 456-503 158-205 (239)
208 smart00351 PAX Paired Box doma 90.9 0.54 1.2E-05 42.4 5.9 42 457-502 18-59 (125)
209 PRK07406 RNA polymerase sigma 90.9 2 4.4E-05 46.0 11.1 36 232-267 223-258 (373)
210 PF08279 HTH_11: HTH domain; 90.4 0.43 9.4E-06 36.2 4.1 39 460-500 1-39 (55)
211 PF12802 MarR_2: MarR family; 90.2 0.59 1.3E-05 36.0 4.8 44 456-500 2-45 (62)
212 PHA00675 hypothetical protein 89.9 0.65 1.4E-05 38.5 4.8 40 456-498 22-61 (78)
213 PF01022 HTH_5: Bacterial regu 89.8 0.65 1.4E-05 34.4 4.5 37 459-499 2-38 (47)
214 PRK07408 RNA polymerase sigma 89.7 1.3 2.7E-05 44.7 7.9 36 233-268 114-149 (256)
215 COG2390 DeoR Transcriptional r 89.6 0.49 1.1E-05 49.6 5.0 35 464-502 18-52 (321)
216 PF02650 HTH_WhiA: WhiA C-term 89.5 0.72 1.6E-05 39.1 5.0 44 454-500 35-80 (85)
217 COG2909 MalT ATP-dependent tra 89.5 0.48 1E-05 55.0 5.2 51 457-512 832-882 (894)
218 PHA02591 hypothetical protein; 89.2 0.46 9.9E-06 39.5 3.5 24 475-498 58-81 (83)
219 PRK00423 tfb transcription ini 88.5 15 0.00033 38.2 15.1 176 281-505 123-305 (310)
220 PF12840 HTH_20: Helix-turn-he 88.2 1.6 3.4E-05 34.0 5.9 39 458-499 9-47 (61)
221 PRK05949 RNA polymerase sigma 87.8 4.5 9.7E-05 42.5 10.8 36 233-268 179-214 (327)
222 cd00131 PAX Paired Box domain 87.6 1.3 2.9E-05 40.1 5.8 42 457-502 18-59 (128)
223 PF01726 LexA_DNA_bind: LexA D 87.1 1.9 4.1E-05 34.6 5.8 42 366-407 7-49 (65)
224 PRK06288 RNA polymerase sigma 87.0 13 0.00028 37.5 13.3 36 233-268 119-154 (268)
225 PRK05911 RNA polymerase sigma 86.8 5.6 0.00012 40.1 10.5 36 234-269 112-147 (257)
226 PF13542 HTH_Tnp_ISL3: Helix-t 86.8 1.5 3.3E-05 32.7 4.9 25 476-500 27-51 (52)
227 TIGR02885 spore_sigF RNA polym 86.5 4.3 9.3E-05 39.8 9.3 33 236-268 101-133 (231)
228 smart00550 Zalpha Z-DNA-bindin 86.5 1.6 3.5E-05 35.1 5.2 24 476-499 22-45 (68)
229 PF01047 MarR: MarR family; I 86.2 1.2 2.6E-05 34.1 4.1 42 457-501 1-42 (59)
230 PF13463 HTH_27: Winged helix 86.1 1.4 3.1E-05 34.4 4.6 43 457-501 1-43 (68)
231 smart00344 HTH_ASNC helix_turn 86.0 1.6 3.5E-05 37.5 5.3 41 457-500 1-41 (108)
232 PRK07122 RNA polymerase sigma 85.8 7.8 0.00017 39.3 11.0 36 234-269 129-164 (264)
233 COG3355 Predicted transcriptio 85.8 2.8 6E-05 38.2 6.8 51 449-505 17-67 (126)
234 PRK10046 dpiA two-component re 85.7 0.82 1.8E-05 44.4 3.7 40 456-499 161-200 (225)
235 PF00356 LacI: Bacterial regul 85.7 0.8 1.7E-05 34.3 2.8 22 478-499 1-22 (46)
236 PRK07405 RNA polymerase sigma 85.6 6.7 0.00015 40.9 10.6 36 233-268 169-204 (317)
237 COG3415 Transposase and inacti 85.3 1.2 2.7E-05 41.1 4.4 37 460-501 10-46 (138)
238 PF01325 Fe_dep_repress: Iron 85.3 1.1 2.4E-05 35.2 3.6 42 457-498 2-44 (60)
239 PF01978 TrmB: Sugar-specific 85.2 0.59 1.3E-05 37.1 2.0 41 456-499 5-45 (68)
240 PHA02547 55 RNA polymerase sig 85.2 6.8 0.00015 37.4 9.2 62 283-347 46-110 (179)
241 TIGR02850 spore_sigG RNA polym 84.9 9.5 0.00021 38.2 11.0 35 235-269 123-157 (254)
242 TIGR02147 Fsuc_second hypothet 84.8 10 0.00023 38.8 11.3 107 382-493 135-246 (271)
243 TIGR02997 Sig70-cyanoRpoD RNA 84.6 9.3 0.0002 39.3 11.1 35 234-268 163-197 (298)
244 PF12728 HTH_17: Helix-turn-he 84.6 1 2.2E-05 33.6 3.0 24 477-500 2-25 (51)
245 PF01418 HTH_6: Helix-turn-hel 84.4 1.7 3.8E-05 35.6 4.5 52 447-498 4-56 (77)
246 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 84.3 2 4.3E-05 32.9 4.4 39 456-498 4-42 (50)
247 PF03444 HrcA_DNA-bdg: Winged 84.3 2.3 4.9E-05 35.5 5.1 43 456-498 1-45 (78)
248 PF01371 Trp_repressor: Trp re 84.1 1.2 2.7E-05 37.9 3.6 46 457-503 27-75 (87)
249 PRK07500 rpoH2 RNA polymerase 84.0 9.8 0.00021 39.1 10.9 25 383-407 244-268 (289)
250 PF13011 LZ_Tnp_IS481: leucine 83.8 2.4 5.3E-05 35.9 5.2 43 456-501 8-50 (85)
251 TIGR02479 FliA_WhiG RNA polyme 83.6 14 0.00031 36.0 11.4 37 233-269 84-120 (224)
252 PF09339 HTH_IclR: IclR helix- 83.1 1.6 3.4E-05 33.0 3.5 27 472-498 14-40 (52)
253 PRK13413 mpi multiple promoter 83.0 2 4.4E-05 41.4 5.1 35 460-499 161-195 (200)
254 PRK11083 DNA-binding response 82.9 1.7 3.6E-05 41.0 4.4 50 456-506 154-208 (228)
255 cd04762 HTH_MerR-trunc Helix-T 82.8 1.5 3.2E-05 31.4 3.1 25 477-501 1-25 (49)
256 PRK10336 DNA-binding transcrip 82.6 1.7 3.7E-05 40.8 4.3 50 456-506 149-203 (219)
257 smart00342 HTH_ARAC helix_turn 82.6 17 0.00036 28.6 9.6 74 384-500 1-75 (84)
258 TIGR00498 lexA SOS regulatory 82.4 1.9 4.2E-05 41.4 4.7 45 455-499 2-49 (199)
259 TIGR01764 excise DNA binding d 82.3 1.5 3.3E-05 31.6 3.1 24 477-500 2-25 (49)
260 PRK10710 DNA-binding transcrip 82.1 2 4.3E-05 41.0 4.7 50 456-506 160-214 (240)
261 TIGR01610 phage_O_Nterm phage 82.0 5.3 0.00011 34.2 6.8 48 455-506 21-73 (95)
262 smart00345 HTH_GNTR helix_turn 81.7 2.5 5.3E-05 31.8 4.1 29 474-506 17-46 (60)
263 PRK12423 LexA repressor; Provi 81.4 2.3 4.9E-05 41.4 4.8 48 455-506 2-52 (202)
264 PRK07670 RNA polymerase sigma 81.2 17 0.00036 36.3 11.1 37 233-269 110-146 (251)
265 PF08220 HTH_DeoR: DeoR-like h 80.9 2.3 5.1E-05 32.9 3.8 25 474-498 12-36 (57)
266 PRK11179 DNA-binding transcrip 80.8 3.3 7.2E-05 38.3 5.5 41 456-499 6-46 (153)
267 TIGR02337 HpaR homoprotocatech 80.7 6.6 0.00014 34.4 7.1 49 448-499 15-65 (118)
268 PRK15479 transcriptional regul 80.7 2.7 5.9E-05 39.3 5.0 50 456-506 148-202 (221)
269 PF02954 HTH_8: Bacterial regu 80.4 2.4 5.2E-05 30.8 3.5 38 459-499 4-41 (42)
270 PF13551 HTH_29: Winged helix- 80.3 3.1 6.8E-05 35.5 4.8 26 475-500 10-36 (112)
271 cd04761 HTH_MerR-SF Helix-Turn 80.2 1.3 2.9E-05 32.3 2.1 25 477-501 1-25 (49)
272 smart00420 HTH_DEOR helix_turn 79.8 3.7 8E-05 29.9 4.4 25 475-499 13-37 (53)
273 PF13744 HTH_37: Helix-turn-he 78.9 3 6.5E-05 34.5 4.1 25 474-498 29-53 (80)
274 PRK11169 leucine-responsive tr 78.8 3.3 7.1E-05 38.9 4.8 40 457-499 12-51 (164)
275 PF01381 HTH_3: Helix-turn-hel 78.8 2.1 4.5E-05 32.1 2.9 25 475-499 8-32 (55)
276 TIGR03787 marine_sort_RR prote 78.3 3.3 7.1E-05 39.3 4.7 50 456-506 156-207 (227)
277 TIGR02787 codY_Gpos GTP-sensin 77.9 8.4 0.00018 38.9 7.5 56 447-506 167-224 (251)
278 COG0856 Orotate phosphoribosyl 77.9 2.9 6.2E-05 40.2 4.0 41 463-508 10-50 (203)
279 COG1522 Lrp Transcriptional re 77.6 4.6 9.9E-05 36.8 5.3 43 455-500 4-46 (154)
280 COG2522 Predicted transcriptio 77.3 4 8.7E-05 36.8 4.6 24 475-498 21-44 (119)
281 PF13411 MerR_1: MerR HTH fami 77.0 1.3 2.7E-05 35.0 1.2 25 477-501 1-25 (69)
282 PF00046 Homeobox: Homeobox do 76.9 4.8 0.0001 30.5 4.4 50 456-505 6-56 (57)
283 smart00419 HTH_CRP helix_turn_ 76.7 3.5 7.7E-05 29.7 3.5 27 476-506 8-34 (48)
284 PHA01976 helix-turn-helix prot 76.6 4.1 8.8E-05 31.9 4.1 26 474-499 13-38 (67)
285 TIGR02154 PhoB phosphate regul 76.6 1.7 3.8E-05 40.7 2.3 51 456-507 154-209 (226)
286 PRK00215 LexA repressor; Valid 76.5 4.3 9.3E-05 39.2 5.0 45 457-501 2-49 (205)
287 PRK08215 sporulation sigma fac 76.1 30 0.00066 34.6 11.2 33 236-268 127-159 (258)
288 PF08280 HTH_Mga: M protein tr 76.0 4.2 9.1E-05 31.7 3.9 37 460-499 6-42 (59)
289 PHA00542 putative Cro-like pro 74.8 3.9 8.5E-05 34.1 3.7 26 475-500 30-55 (82)
290 cd00092 HTH_CRP helix_turn_hel 74.8 4.8 0.0001 31.1 4.0 25 475-499 24-48 (67)
291 PF13022 HTH_Tnp_1_2: Helix-tu 74.7 8.4 0.00018 35.7 6.1 49 450-498 4-56 (142)
292 PF13560 HTH_31: Helix-turn-he 74.5 3.9 8.4E-05 32.0 3.4 25 475-499 13-37 (64)
293 TIGR03070 couple_hipB transcri 74.5 3.4 7.3E-05 30.8 3.0 25 475-499 14-38 (58)
294 TIGR00122 birA_repr_reg BirA b 74.4 6.8 0.00015 31.1 4.9 25 475-499 12-36 (69)
295 COG1476 Predicted transcriptio 74.3 4.9 0.00011 32.7 3.9 25 475-499 13-37 (68)
296 PF08822 DUF1804: Protein of u 74.2 6.6 0.00014 37.3 5.4 41 459-502 5-45 (165)
297 PRK11564 stationary phase indu 74.2 6.7 0.00014 42.3 6.3 51 456-506 10-60 (426)
298 PF13545 HTH_Crp_2: Crp-like h 74.0 3.6 7.8E-05 32.9 3.2 27 476-506 28-54 (76)
299 PRK11512 DNA-binding transcrip 73.6 14 0.00031 33.5 7.4 48 449-499 28-77 (144)
300 COG1508 RpoN DNA-directed RNA 73.6 81 0.0017 34.7 14.1 55 444-498 283-352 (444)
301 PF13551 HTH_29: Winged helix- 73.3 9.6 0.00021 32.4 5.9 23 386-408 14-36 (112)
302 TIGR02844 spore_III_D sporulat 73.1 6.7 0.00015 32.9 4.6 24 475-498 18-41 (80)
303 TIGR01884 cas_HTH CRISPR locus 73.1 8.9 0.00019 37.2 6.3 44 453-499 137-180 (203)
304 PF00376 MerR: MerR family reg 73.1 2.1 4.6E-05 30.6 1.5 24 478-501 1-24 (38)
305 PF08765 Mor: Mor transcriptio 72.8 7.3 0.00016 34.1 5.1 42 460-507 62-103 (108)
306 TIGR02941 Sigma_B RNA polymera 72.7 31 0.00068 34.3 10.3 33 235-267 119-151 (255)
307 TIGR03697 NtcA_cyano global ni 72.5 3.9 8.5E-05 38.3 3.6 28 476-507 143-170 (193)
308 smart00347 HTH_MARR helix_turn 72.4 8.2 0.00018 31.8 5.2 41 456-499 7-47 (101)
309 COG4367 Uncharacterized protei 72.3 11 0.00023 32.2 5.6 54 457-517 3-60 (97)
310 cd07377 WHTH_GntR Winged helix 72.2 7.4 0.00016 29.7 4.5 26 477-506 26-51 (66)
311 TIGR02612 mob_myst_A mobile my 72.1 7.2 0.00016 36.5 5.1 38 458-499 24-61 (150)
312 cd01104 HTH_MlrA-CarA Helix-Tu 71.9 4.7 0.0001 31.6 3.4 23 477-499 1-23 (68)
313 PRK13239 alkylmercury lyase; P 71.7 7.9 0.00017 38.1 5.5 29 381-409 33-61 (206)
314 TIGR03830 CxxCG_CxxCG_HTH puta 71.6 11 0.00025 33.1 6.2 40 455-500 63-102 (127)
315 PF07750 GcrA: GcrA cell cycle 71.5 4.6 9.9E-05 38.3 3.7 37 459-499 5-42 (162)
316 PRK11302 DNA-binding transcrip 71.5 6.3 0.00014 39.7 5.0 51 447-499 4-57 (284)
317 cd06571 Bac_DnaA_C C-terminal 71.3 13 0.00028 31.3 6.1 32 475-506 43-75 (90)
318 PRK05572 sporulation sigma fac 71.3 44 0.00095 33.3 11.0 32 235-266 121-152 (252)
319 CHL00148 orf27 Ycf27; Reviewed 71.3 5.4 0.00012 37.9 4.3 50 456-506 161-217 (240)
320 COG0568 RpoD DNA-directed RNA 71.0 54 0.0012 34.8 11.8 36 233-268 190-225 (342)
321 cd00086 homeodomain Homeodomai 70.6 13 0.00028 27.9 5.5 51 456-506 6-57 (59)
322 cd00090 HTH_ARSR Arsenical Res 70.4 10 0.00022 29.1 5.0 37 459-499 7-43 (78)
323 PRK10072 putative transcriptio 70.1 6 0.00013 34.3 3.8 25 475-499 45-69 (96)
324 PF01527 HTH_Tnp_1: Transposas 69.8 4.8 0.0001 32.2 3.0 27 475-501 22-48 (76)
325 PF14493 HTH_40: Helix-turn-he 69.8 11 0.00023 31.9 5.3 29 475-503 12-40 (91)
326 PRK11337 DNA-binding transcrip 69.7 7.8 0.00017 39.4 5.3 53 445-499 14-69 (292)
327 smart00418 HTH_ARSR helix_turn 69.6 9.3 0.0002 28.5 4.5 26 475-500 9-34 (66)
328 smart00346 HTH_ICLR helix_turn 69.3 10 0.00023 31.2 5.1 26 475-500 19-44 (91)
329 PRK11511 DNA-binding transcrip 69.3 55 0.0012 29.2 10.1 41 367-407 8-48 (127)
330 PRK10870 transcriptional repre 69.2 23 0.00049 33.7 8.0 52 448-500 42-95 (176)
331 COG1654 BirA Biotin operon rep 69.2 9.4 0.0002 32.0 4.7 30 473-506 16-45 (79)
332 PRK06986 fliA flagellar biosyn 69.1 58 0.0013 32.0 11.2 33 236-268 99-131 (236)
333 cd04764 HTH_MlrA-like_sg1 Heli 69.0 6 0.00013 31.1 3.4 24 477-500 1-24 (67)
334 PF08535 KorB: KorB domain; I 68.4 5 0.00011 34.0 3.0 24 475-498 2-25 (93)
335 PF12324 HTH_15: Helix-turn-he 68.4 13 0.00029 31.0 5.3 29 381-409 35-63 (77)
336 PRK06596 RNA polymerase factor 68.4 64 0.0014 33.0 11.6 25 383-407 247-271 (284)
337 PRK09413 IS2 repressor TnpA; R 68.1 11 0.00025 33.5 5.4 28 474-501 27-54 (121)
338 COG2345 Predicted transcriptio 67.1 10 0.00022 37.7 5.2 26 474-499 23-48 (218)
339 PRK10141 DNA-binding transcrip 66.8 18 0.00038 32.5 6.2 45 451-498 7-52 (117)
340 PRK15482 transcriptional regul 66.5 9.6 0.00021 38.7 5.1 50 448-499 5-57 (285)
341 smart00422 HTH_MERR helix_turn 66.5 4.4 9.6E-05 31.8 2.1 25 477-501 1-25 (70)
342 PRK09863 putative frv operon r 66.2 37 0.00081 38.3 10.2 103 383-505 16-121 (584)
343 smart00354 HTH_LACI helix_turn 66.1 5.9 0.00013 31.8 2.8 22 477-498 1-22 (70)
344 TIGR01889 Staph_reg_Sar staphy 66.1 15 0.00033 31.9 5.6 45 456-500 22-67 (109)
345 PRK00135 scpB segregation and 65.9 40 0.00086 32.7 9.0 104 374-490 9-118 (188)
346 cd04763 HTH_MlrA-like Helix-Tu 65.8 7.5 0.00016 30.7 3.3 23 477-499 1-23 (68)
347 PF14394 DUF4423: Domain of un 65.3 12 0.00026 35.7 5.2 103 382-489 37-144 (171)
348 TIGR00647 MG103 conserved hypo 65.2 13 0.00028 38.3 5.8 44 454-500 225-274 (279)
349 COG2973 TrpR Trp operon repres 65.0 12 0.00025 32.6 4.5 45 457-505 38-85 (103)
350 COG2944 Predicted transcriptio 64.8 13 0.00029 32.7 4.9 40 454-499 41-80 (104)
351 PRK11557 putative DNA-binding 64.2 8.6 0.00019 38.8 4.3 48 450-499 3-53 (278)
352 PHA00738 putative HTH transcri 64.0 15 0.00032 32.7 5.0 38 458-498 11-48 (108)
353 PF00392 GntR: Bacterial regul 63.9 8.1 0.00018 30.2 3.2 28 474-505 21-49 (64)
354 smart00389 HOX Homeodomain. DN 63.7 16 0.00036 27.2 4.8 48 456-503 6-54 (56)
355 COG1318 Predicted transcriptio 63.5 7.2 0.00016 37.3 3.2 26 475-500 60-85 (182)
356 PF04963 Sigma54_CBD: Sigma-54 62.8 2.5 5.4E-05 41.0 0.1 95 384-504 52-146 (194)
357 PF02082 Rrf2: Transcriptional 62.6 13 0.00029 30.7 4.4 24 476-499 25-48 (83)
358 PF11662 DUF3263: Protein of u 62.5 26 0.00057 29.2 6.0 46 456-501 2-47 (77)
359 COG1405 SUA7 Transcription ini 62.2 2E+02 0.0043 29.8 14.6 28 475-502 250-277 (285)
360 PRK01905 DNA-binding protein F 61.8 30 0.00065 28.4 6.3 37 460-499 37-73 (77)
361 PF00165 HTH_AraC: Bacterial r 61.8 12 0.00026 26.7 3.5 27 474-500 6-32 (42)
362 PRK10411 DNA-binding transcrip 61.3 14 0.00031 36.9 5.2 41 459-502 4-44 (240)
363 COG4367 Uncharacterized protei 61.2 22 0.00047 30.5 5.3 39 372-410 10-49 (97)
364 COG5484 Uncharacterized conser 60.7 10 0.00022 38.5 3.8 25 475-499 18-42 (279)
365 TIGR02607 antidote_HigA addict 60.6 9.3 0.0002 30.7 3.1 25 475-499 17-41 (78)
366 COG1737 RpiR Transcriptional r 60.5 13 0.00028 38.0 4.8 52 445-498 4-58 (281)
367 PRK13918 CRP/FNR family transc 59.9 9.3 0.0002 36.1 3.4 27 476-506 149-175 (202)
368 PF01710 HTH_Tnp_IS630: Transp 59.3 8.4 0.00018 34.3 2.8 24 475-498 70-93 (119)
369 PF12844 HTH_19: Helix-turn-he 58.7 9.7 0.00021 29.4 2.8 25 475-499 11-35 (64)
370 PRK09744 DNA-binding transcrip 58.7 13 0.00028 30.8 3.4 19 478-496 12-30 (75)
371 PF12116 SpoIIID: Stage III sp 58.3 11 0.00023 31.8 3.0 42 461-504 6-47 (82)
372 PF04703 FaeA: FaeA-like prote 58.3 9.8 0.00021 30.4 2.7 25 475-499 14-38 (62)
373 PF01710 HTH_Tnp_IS630: Transp 58.0 12 0.00026 33.2 3.6 25 474-498 16-40 (119)
374 PRK03573 transcriptional regul 57.9 27 0.00058 31.6 6.0 49 449-499 19-69 (144)
375 PF00440 TetR_N: Bacterial reg 57.5 18 0.00039 26.5 3.9 23 474-496 14-36 (47)
376 PF05043 Mga: Mga helix-turn-h 57.4 6.5 0.00014 32.6 1.7 33 474-506 28-60 (87)
377 PRK14101 bifunctional glucokin 57.4 16 0.00034 41.8 5.3 53 445-499 342-397 (638)
378 COG1510 Predicted transcriptio 57.3 11 0.00023 36.2 3.2 29 474-506 39-67 (177)
379 PRK09726 antitoxin HipB; Provi 57.0 11 0.00024 31.5 3.1 25 475-499 24-48 (88)
380 KOG0484 Transcription factor P 56.8 14 0.00031 32.5 3.7 53 455-511 27-79 (125)
381 PF08784 RPA_C: Replication pr 56.4 18 0.0004 31.0 4.4 44 456-499 44-88 (102)
382 PF07037 DUF1323: Putative tra 56.4 12 0.00026 33.7 3.3 23 477-499 1-23 (122)
383 PF06322 Phage_NinH: Phage Nin 56.3 16 0.00035 29.1 3.5 28 464-498 11-38 (64)
384 COG3877 Uncharacterized protei 56.2 22 0.00047 31.5 4.7 48 455-506 40-87 (122)
385 cd04768 HTH_BmrR-like Helix-Tu 56.1 8.3 0.00018 33.0 2.1 26 477-502 1-26 (96)
386 smart00530 HTH_XRE Helix-turn- 55.8 14 0.0003 25.8 3.1 25 475-499 9-33 (56)
387 PRK12427 flagellar biosynthesi 55.8 26 0.00057 34.7 6.0 36 234-269 103-138 (231)
388 cd01392 HTH_LacI Helix-turn-he 55.4 7.8 0.00017 28.6 1.7 19 481-499 2-20 (52)
389 PRK09391 fixK transcriptional 54.8 13 0.00028 36.5 3.6 27 476-506 179-205 (230)
390 PRK13777 transcriptional regul 54.8 50 0.0011 32.0 7.5 40 456-498 42-81 (185)
391 COG1846 MarR Transcriptional r 54.5 23 0.0005 30.0 4.7 41 457-500 20-60 (126)
392 TIGR02392 rpoH_proteo alternat 53.9 1.1E+02 0.0023 31.0 10.1 26 382-407 234-259 (270)
393 cd04775 HTH_Cfa-like Helix-Tur 53.9 9.2 0.0002 33.1 2.1 26 477-502 2-27 (102)
394 TIGR02944 suf_reg_Xantho FeS a 53.5 20 0.00044 31.9 4.4 26 474-499 23-48 (130)
395 PRK04984 fatty acid metabolism 53.2 18 0.00038 35.6 4.3 29 474-506 28-57 (239)
396 cd01107 HTH_BmrR Helix-Turn-He 53.2 10 0.00022 33.2 2.2 26 477-502 1-26 (108)
397 cd04773 HTH_TioE_rpt2 Second H 53.0 9.8 0.00021 33.3 2.1 25 477-501 1-25 (108)
398 PRK10955 DNA-binding transcrip 53.0 10 0.00022 35.8 2.5 46 456-506 156-210 (232)
399 PF05225 HTH_psq: helix-turn-h 52.8 33 0.00072 25.3 4.6 23 477-499 17-39 (45)
400 PF00292 PAX: 'Paired box' dom 52.7 28 0.00061 31.7 5.0 34 462-500 24-57 (125)
401 PRK09706 transcriptional repre 52.4 14 0.0003 33.4 3.1 25 475-499 17-41 (135)
402 PF13443 HTH_26: Cro/C1-type H 52.2 14 0.0003 28.4 2.7 26 475-500 9-34 (63)
403 PRK11161 fumarate/nitrate redu 51.9 15 0.00032 35.8 3.4 27 476-506 184-210 (235)
404 PRK11753 DNA-binding transcrip 51.8 16 0.00034 34.7 3.6 27 476-506 168-194 (211)
405 cd04782 HTH_BltR Helix-Turn-He 51.7 11 0.00023 32.3 2.1 25 477-501 1-25 (97)
406 PF14549 P22_Cro: DNA-binding 51.7 20 0.00043 28.4 3.5 19 478-496 11-29 (60)
407 COG2512 Predicted membrane-ass 51.6 22 0.00047 36.3 4.6 43 455-499 191-233 (258)
408 PRK13509 transcriptional repre 51.4 23 0.0005 35.6 4.8 38 459-499 5-42 (251)
409 PF13556 HTH_30: PucR C-termin 51.3 34 0.00075 26.4 4.8 34 474-507 10-43 (59)
410 PRK10434 srlR DNA-bindng trans 51.2 22 0.00047 35.9 4.6 41 459-503 5-45 (256)
411 TIGR02698 CopY_TcrY copper tra 51.0 39 0.00084 30.6 5.8 45 456-503 1-49 (130)
412 cd04788 HTH_NolA-AlbR Helix-Tu 51.0 11 0.00024 32.2 2.1 26 477-502 1-26 (96)
413 COG4465 CodY Pleiotropic trans 50.9 47 0.001 33.1 6.6 56 448-507 174-231 (261)
414 cd01105 HTH_GlnR-like Helix-Tu 50.7 11 0.00025 31.6 2.1 25 477-501 2-26 (88)
415 cd04789 HTH_Cfa Helix-Turn-Hel 50.6 11 0.00025 32.5 2.2 26 477-502 2-27 (102)
416 PRK03902 manganese transport t 50.5 25 0.00054 32.0 4.5 25 475-499 21-45 (142)
417 cd04772 HTH_TioE_rpt1 First He 50.4 12 0.00026 32.3 2.2 26 477-502 1-26 (99)
418 cd01109 HTH_YyaN Helix-Turn-He 50.3 12 0.00025 32.9 2.2 26 477-502 1-26 (113)
419 cd04780 HTH_MerR-like_sg5 Heli 50.2 12 0.00025 32.1 2.1 25 477-501 1-25 (95)
420 PF12298 Bot1p: Eukaryotic mit 50.2 31 0.00068 33.1 5.2 39 457-498 17-55 (172)
421 cd04766 HTH_HspR Helix-Turn-He 50.1 11 0.00025 31.6 2.0 26 477-502 2-27 (91)
422 COG1321 TroR Mn-dependent tran 49.9 28 0.0006 32.7 4.7 43 457-499 4-47 (154)
423 PRK11414 colanic acid/biofilm 49.8 19 0.0004 35.1 3.8 30 473-506 31-60 (221)
424 TIGR02812 fadR_gamma fatty aci 49.6 22 0.00047 34.9 4.3 30 473-506 26-56 (235)
425 cd04765 HTH_MlrA-like_sg2 Heli 49.6 19 0.00042 31.1 3.4 23 477-499 1-23 (99)
426 PRK11050 manganese transport r 49.5 25 0.00054 32.6 4.4 26 475-500 50-75 (152)
427 cd04774 HTH_YfmP Helix-Turn-He 49.3 12 0.00026 32.1 2.1 26 477-502 1-26 (96)
428 smart00352 POU Found in Pit-Oc 49.2 26 0.00056 29.1 3.9 25 475-499 23-53 (75)
429 cd01282 HTH_MerR-like_sg3 Heli 49.2 12 0.00027 32.8 2.2 26 477-502 1-26 (112)
430 TIGR00180 parB_part ParB-like 49.2 29 0.00063 33.2 4.9 44 455-500 101-144 (187)
431 PRK09990 DNA-binding transcrip 48.5 23 0.0005 35.1 4.3 38 463-506 19-57 (251)
432 TIGR03338 phnR_burk phosphonat 48.3 21 0.00045 34.4 3.8 29 474-506 32-60 (212)
433 cd00093 HTH_XRE Helix-turn-hel 48.0 30 0.00065 24.2 3.8 25 475-499 11-35 (58)
434 cd01106 HTH_TipAL-Mta Helix-Tu 48.0 13 0.00029 32.0 2.2 25 477-501 1-25 (103)
435 PRK11534 DNA-binding transcrip 47.9 24 0.00052 34.3 4.2 39 462-506 18-56 (224)
436 cd00592 HTH_MerR-like Helix-Tu 47.8 14 0.00029 31.4 2.2 25 477-501 1-25 (100)
437 COG3093 VapI Plasmid maintenan 47.5 29 0.00063 30.6 4.1 35 463-499 12-46 (104)
438 TIGR02395 rpoN_sigma RNA polym 47.3 23 0.00051 38.6 4.4 25 474-498 316-340 (429)
439 cd01279 HTH_HspR-like Helix-Tu 47.3 13 0.00029 31.9 2.0 25 477-501 2-26 (98)
440 cd04777 HTH_MerR-like_sg1 Heli 47.2 14 0.00031 32.0 2.2 26 477-502 1-26 (107)
441 cd04769 HTH_MerR2 Helix-Turn-H 47.1 14 0.0003 32.7 2.2 27 477-503 1-27 (116)
442 PF06413 Neugrin: Neugrin; In 47.0 31 0.00068 34.5 4.9 42 456-498 10-51 (225)
443 PF09012 FeoC: FeoC like trans 46.7 13 0.00028 29.7 1.8 26 474-499 12-37 (69)
444 TIGR00738 rrf2_super rrf2 fami 46.5 39 0.00084 30.0 5.0 26 474-499 23-48 (132)
445 PF05732 RepL: Firmicute plasm 46.5 46 0.001 31.6 5.7 53 450-506 46-101 (165)
446 PRK10161 transcriptional regul 46.4 23 0.0005 33.5 3.8 50 456-506 154-208 (229)
447 COG3711 BglG Transcriptional a 46.4 44 0.00094 36.6 6.4 115 381-506 16-130 (491)
448 PRK14082 hypothetical protein; 46.4 65 0.0014 26.0 5.5 56 272-332 7-62 (65)
449 cd04783 HTH_MerR1 Helix-Turn-H 46.3 14 0.0003 33.1 2.1 27 477-503 1-27 (126)
450 PF12793 SgrR_N: Sugar transpo 46.3 30 0.00065 30.8 4.2 33 466-499 10-42 (115)
451 PRK03837 transcriptional regul 46.2 28 0.0006 34.1 4.4 29 474-506 34-63 (241)
452 PRK10421 DNA-binding transcrip 46.2 26 0.00057 34.8 4.3 38 463-506 14-52 (253)
453 cd01111 HTH_MerD Helix-Turn-He 46.1 15 0.00032 32.2 2.2 26 477-502 1-26 (107)
454 PRK15121 right oriC-binding tr 46.0 2.3E+02 0.005 28.7 11.2 41 367-407 4-44 (289)
455 PRK06424 transcription factor; 45.9 26 0.00056 32.6 3.8 25 475-499 96-120 (144)
456 smart00342 HTH_ARAC helix_turn 45.9 31 0.00067 27.0 3.9 26 476-501 1-26 (84)
457 cd04770 HTH_HMRTR Helix-Turn-H 45.8 15 0.00033 32.6 2.2 27 477-503 1-27 (123)
458 PRK10643 DNA-binding transcrip 45.6 23 0.00051 32.9 3.6 47 456-505 149-202 (222)
459 PRK11014 transcriptional repre 45.5 28 0.00061 31.7 4.0 29 474-506 23-51 (141)
460 PRK10681 DNA-binding transcrip 45.4 38 0.00082 34.1 5.3 41 459-503 7-47 (252)
461 COG1349 GlpR Transcriptional r 45.3 23 0.00049 35.8 3.7 38 458-498 4-41 (253)
462 PRK13705 plasmid-partitioning 44.9 27 0.00058 37.6 4.3 56 446-501 3-64 (388)
463 PRK13503 transcriptional activ 44.9 1.9E+02 0.004 28.7 10.2 35 373-407 176-210 (278)
464 PF10078 DUF2316: Uncharacteri 44.7 44 0.00095 28.7 4.7 24 475-498 22-45 (89)
465 TIGR02431 pcaR_pcaU beta-ketoa 44.7 36 0.00078 33.8 5.0 26 474-499 22-47 (248)
466 PRK09464 pdhR transcriptional 44.6 29 0.00063 34.4 4.3 39 462-506 21-60 (254)
467 PRK10906 DNA-binding transcrip 44.5 33 0.00071 34.6 4.7 38 459-499 5-42 (252)
468 cd04767 HTH_HspR-like_MBC Heli 44.1 16 0.00035 32.9 2.1 26 477-502 2-27 (120)
469 PF02042 RWP-RK: RWP-RK domain 44.1 51 0.0011 25.5 4.5 28 464-497 9-36 (52)
470 PRK10225 DNA-binding transcrip 44.0 30 0.00064 34.5 4.3 38 463-506 21-59 (257)
471 PRK13890 conjugal transfer pro 44.0 30 0.00065 31.0 3.8 25 475-499 17-41 (120)
472 PF05930 Phage_AlpA: Prophage 43.8 31 0.00067 25.9 3.4 24 477-500 4-27 (51)
473 TIGR00270 conserved hypothetic 43.7 31 0.00066 32.5 4.0 26 474-499 80-105 (154)
474 PRK08359 transcription factor; 43.6 30 0.00064 33.4 3.9 26 474-499 96-121 (176)
475 PRK10572 DNA-binding transcrip 43.5 3.5E+02 0.0076 27.1 15.2 36 372-407 187-222 (290)
476 PRK12469 RNA polymerase factor 43.3 34 0.00073 38.0 4.9 46 453-498 334-391 (481)
477 cd04781 HTH_MerR-like_sg6 Heli 43.3 17 0.00037 32.3 2.2 26 477-502 1-26 (120)
478 TIGR02394 rpoS_proteo RNA poly 43.2 2.8E+02 0.0061 28.2 11.3 32 238-269 139-170 (285)
479 PRK06266 transcription initiat 43.1 66 0.0014 30.9 6.3 39 458-499 21-59 (178)
480 PF02787 CPSase_L_D3: Carbamoy 42.7 2.3E+02 0.005 25.5 9.4 24 476-499 72-95 (123)
481 PRK04424 fatty acid biosynthes 42.5 38 0.00083 32.5 4.6 37 459-498 7-43 (185)
482 PRK09943 DNA-binding transcrip 42.4 32 0.00069 32.7 4.0 25 475-499 19-43 (185)
483 PRK09834 DNA-binding transcrip 42.4 38 0.00082 34.1 4.8 26 474-499 24-49 (263)
484 PRK11886 bifunctional biotin-- 42.2 41 0.00089 34.8 5.1 40 460-502 5-44 (319)
485 cd04776 HTH_GnyR Helix-Turn-He 42.1 18 0.0004 32.2 2.2 25 477-501 1-25 (118)
486 PF08279 HTH_11: HTH domain; 42.0 54 0.0012 24.4 4.5 23 385-407 16-38 (55)
487 PRK10402 DNA-binding transcrip 41.7 52 0.0011 32.0 5.5 46 457-506 149-195 (226)
488 PRK05932 RNA polymerase factor 41.7 32 0.00069 37.9 4.4 45 454-498 309-365 (455)
489 PF04967 HTH_10: HTH DNA bindi 41.6 37 0.0008 26.2 3.5 26 382-407 21-46 (53)
490 PF04552 Sigma54_DBD: Sigma-54 41.4 8.8 0.00019 36.3 0.0 47 450-498 25-71 (160)
491 PF06971 Put_DNA-bind_N: Putat 41.4 48 0.001 25.3 4.0 40 366-405 10-49 (50)
492 TIGR03826 YvyF flagellar opero 41.1 62 0.0013 29.9 5.5 46 367-412 29-74 (137)
493 TIGR02404 trehalos_R_Bsub treh 40.8 29 0.00062 34.0 3.5 26 477-506 25-50 (233)
494 PRK11523 DNA-binding transcrip 40.4 37 0.00081 33.7 4.4 38 463-506 20-58 (253)
495 COG0789 SoxR Predicted transcr 40.4 21 0.00046 31.2 2.3 25 477-501 1-25 (124)
496 PF00325 Crp: Bacterial regula 40.4 36 0.00079 23.6 2.9 22 386-407 4-25 (32)
497 cd04785 HTH_CadR-PbrR-like Hel 40.3 20 0.00043 32.2 2.1 27 477-503 1-27 (126)
498 TIGR01387 cztR_silR_copR heavy 40.3 39 0.00085 31.3 4.3 50 456-506 147-201 (218)
499 COG1481 Uncharacterized protei 40.2 54 0.0012 34.3 5.5 43 454-499 251-295 (308)
500 PF14747 DUF4473: Domain of un 40.2 2.2E+02 0.0047 23.7 8.2 71 384-469 5-79 (82)
No 1
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=100.00 E-value=6.3e-64 Score=527.77 Aligned_cols=314 Identities=31% Similarity=0.489 Sum_probs=290.6
Q ss_pred hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHH--------------------HHHHHHHHHHHhCCCCCHHHH
Q 010092 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKV--------------------FVQVKEQLQKDLGREPTDVEL 254 (518)
Q Consensus 195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~--------------------l~~~~~~l~~~l~r~p~~~el 254 (518)
....++|+|+.||++|+++|+||++||+.|+++||.++. |+++++.|+..+|++|+..||
T Consensus 54 ~~~~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ew 133 (415)
T PRK07598 54 RNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERW 133 (415)
T ss_pred cCCCCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHH
Confidence 346778999999999999999999999999999999998 889999999999999999999
Q ss_pred HHHcc----------------------CCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHH
Q 010092 255 AEATN----------------------MSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312 (518)
Q Consensus 255 a~~~~----------------------~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~ 312 (518)
|.++| |+.++|.+.+..|..|+++||.+|+++|+++|++|. ++|++++||||||+
T Consensus 134 a~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~---~~g~~~eDLiQEG~ 210 (415)
T PRK07598 134 AKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQ---NRGLELLDLVQEGT 210 (415)
T ss_pred HHHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHH
Confidence 95554 555566666677789999999999999999999998 78999999999999
Q ss_pred HHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 010092 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391 (518)
Q Consensus 313 IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA 391 (518)
+|||+|+++|||++|++|||||+||||++|.++++ ++++||+|.|+.+ .+++++++...|.+++||.||.+|||
T Consensus 211 iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e-----~l~~lrk~~r~L~~~lgR~pt~~EiA 285 (415)
T PRK07598 211 LGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITE-----KLNKIKKAQRKISQEKGRTPTIEDIA 285 (415)
T ss_pred HHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence 99999999999999999999999999999999999 8999999999999 99999999999999999999999999
Q ss_pred HHhCCCHHHHHHHHHhcCCccccCCCcCCchhh-hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhc
Q 010092 392 QGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFG 470 (518)
Q Consensus 392 ~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee-l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryG 470 (518)
+.+|+++++|+.++.....++|||.+++.+++. +.+.+. ++..+|++.+....+...|..+|..|||+|+.||.|+||
T Consensus 286 ~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~-~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRyg 364 (415)
T PRK07598 286 QELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFG 364 (415)
T ss_pred HHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Confidence 999999999999999999999999998766654 444443 344567888888889999999999999999999999999
Q ss_pred CCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092 471 LDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517 (518)
Q Consensus 471 L~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~ 517 (518)
|+|++++|++|||+.||+|+++|++++++|++|||++.+...|++|+
T Consensus 365 l~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~ 411 (415)
T PRK07598 365 LADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL 411 (415)
T ss_pred cCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999997
No 2
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=6.1e-60 Score=494.09 Aligned_cols=311 Identities=33% Similarity=0.539 Sum_probs=292.1
Q ss_pred CcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHH
Q 010092 199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278 (518)
Q Consensus 199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~ 278 (518)
..|.+..||++|+++|+||++||..|++.++.+..++..+.+|+...|+.|+..+||.+.|++...|.+.+..|..|++.
T Consensus 61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~ 140 (373)
T PRK07406 61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK 140 (373)
T ss_pred CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence 45889999999999999999999999999999999999999999999999999999999999999999999888999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG 357 (518)
Q Consensus 279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~ 357 (518)
||.+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.|
T Consensus 141 Li~~~l~lV~~iA~ry~---~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~ 217 (373)
T PRK07406 141 MVQSNLRLVVSIAKKYM---NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH 217 (373)
T ss_pred HHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHH
Confidence 99999999999999999 7899999999999999999999999999999999999999999999999 8999999999
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCc
Q 010092 358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVE 436 (518)
Q Consensus 358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~ 436 (518)
+.. .+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+++.+++ .+.+.+.++ ..+
T Consensus 218 ~~~-----~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~-~~~ 291 (373)
T PRK07406 218 LYE-----TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GET 291 (373)
T ss_pred HHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC-CCC
Confidence 998 9999999999999999999999999999999999999999988999999999765544 355555543 345
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092 437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQH 516 (518)
Q Consensus 437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y 516 (518)
|++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||++.....|..|
T Consensus 292 pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~ 371 (373)
T PRK07406 292 PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEY 371 (373)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHH
Confidence 77777888889999999999999999999999999988899999999999999999999999999999999999999999
Q ss_pred cC
Q 010092 517 MV 518 (518)
Q Consensus 517 ~~ 518 (518)
+.
T Consensus 372 ~~ 373 (373)
T PRK07406 372 IR 373 (373)
T ss_pred hC
Confidence 74
No 3
>PRK05949 RNA polymerase sigma factor; Validated
Probab=100.00 E-value=1.1e-59 Score=486.15 Aligned_cols=309 Identities=33% Similarity=0.541 Sum_probs=288.1
Q ss_pred CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (518)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e 277 (518)
.++|.+..||++|+++|+||++||..|++.++.+..+++.++.|+..+|++|+..+||.+++|+..++...+..|..|++
T Consensus 15 ~~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~ 94 (327)
T PRK05949 15 FSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ 94 (327)
T ss_pred CCCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence 35799999999999999999999999999999999999999999999999999999999999999888888887789999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
.||.+|+++|+++|++|. +++.+++|||||||+|||+|+++|||++|++|||||+||||++|.+++. ++++||+|.
T Consensus 95 ~Li~~~~~~V~~iA~~y~---~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~ 171 (327)
T PRK05949 95 KMIEANLRLVVAIAKKYQ---KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPI 171 (327)
T ss_pred HHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCH
Confidence 999999999999999999 7899999999999999999999999999999999999999999999999 899999999
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~ 435 (518)
|+.. .+++++++...+..++||.||++|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++ ..
T Consensus 172 ~~~~-----~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~-~~ 245 (327)
T PRK05949 172 HITE-----KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GP 245 (327)
T ss_pred HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC-CC
Confidence 9999 9999999999999999999999999999999999999999999999999999865544 344545544 35
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 515 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~ 515 (518)
+|++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|+|++.+|++|||+ ....|..
T Consensus 246 ~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~--~~~~l~~ 323 (327)
T PRK05949 246 SPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKE 323 (327)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH--HHHHHHH
Confidence 67878888888999999999999999999999999999999999999999999999999999999999998 4567787
Q ss_pred hc
Q 010092 516 HM 517 (518)
Q Consensus 516 y~ 517 (518)
|+
T Consensus 324 ~~ 325 (327)
T PRK05949 324 YL 325 (327)
T ss_pred HH
Confidence 75
No 4
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=100.00 E-value=3.1e-58 Score=469.94 Aligned_cols=296 Identities=38% Similarity=0.613 Sum_probs=276.5
Q ss_pred ChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHH
Q 010092 201 DLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLI 280 (518)
Q Consensus 201 d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI 280 (518)
|.+..|+++|+.+|+||++||..|++.++.+..+++.+..|+...|++|+..+||+++|++...+...+..|..|+++||
T Consensus 1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv 80 (298)
T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80 (298)
T ss_pred CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999888888887799999999
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~ 359 (518)
.+|+++|+++|++|. ++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. ++++||+|.++.
T Consensus 81 ~~~lrlV~~iA~~y~---~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~ 157 (298)
T TIGR02997 81 KANLRLVVSVAKKYQ---NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHIT 157 (298)
T ss_pred HHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHH
Confidence 999999999999999 7899999999999999999999999999999999999999999999999 899999999999
Q ss_pred chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCcch
Q 010092 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENE 438 (518)
Q Consensus 360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~e 438 (518)
. .+++++++...+...+|+.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.+ ...+|+
T Consensus 158 ~-----~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~-~~~~pe 231 (298)
T TIGR02997 158 E-----KLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPE 231 (298)
T ss_pred H-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccC-CCCCHH
Confidence 8 9999999999999999999999999999999999999999999999999998755443 34444444 345677
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 439 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 439 e~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
+.+...++...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++++|++|||
T Consensus 232 ~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 232 EQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 7788888889999999999999999999999999999999999999999999999999999999997
No 5
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=6.1e-58 Score=471.51 Aligned_cols=309 Identities=33% Similarity=0.543 Sum_probs=286.9
Q ss_pred CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (518)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e 277 (518)
+++|.+..||++|+.+|+||++||..|++.++.+..+++.+..|++.+|++|+..+||.+++++...+...+.+|..|++
T Consensus 5 ~~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~ 84 (317)
T PRK07405 5 TSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR 84 (317)
T ss_pred CCCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence 45789999999999999999999999999999999999999999999999999999999999999888888877789999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
+||.+|+++|+++|++|. +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|. ++++||+|.
T Consensus 85 ~L~~~~~~~V~~~a~~~~---~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~ 161 (317)
T PRK07405 85 KMVEANLRLVVSVAKKYL---KRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI 161 (317)
T ss_pred HHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCCh
Confidence 999999999999999999 7899999999999999999999999999999999999999999999999 899999999
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~ 435 (518)
|+.. .+++++++...+...+|+.||.+|||+.+|++++++..++......+|||.+.+++++ .+.+.+.++ ..
T Consensus 162 ~~~~-----~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~-~~ 235 (317)
T PRK07405 162 HITE-----KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GA 235 (317)
T ss_pred HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC-CC
Confidence 9998 9999999999999999999999999999999999999999988899999998765544 344445443 35
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 515 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~ 515 (518)
+|++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+. ...|..
T Consensus 236 ~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~ 313 (317)
T PRK07405 236 SPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQE 313 (317)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHH
Confidence 678888888899999999999999999999999999999999999999999999999999999999999984 466777
Q ss_pred hc
Q 010092 516 HM 517 (518)
Q Consensus 516 y~ 517 (518)
|+
T Consensus 314 ~~ 315 (317)
T PRK07405 314 YL 315 (317)
T ss_pred HH
Confidence 65
No 6
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=100.00 E-value=2.1e-58 Score=472.31 Aligned_cols=314 Identities=35% Similarity=0.532 Sum_probs=282.1
Q ss_pred cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHccC
Q 010092 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQK-DLGREPTDV---------------ELAEATNM 260 (518)
Q Consensus 197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~-~l~r~p~~~---------------ela~~~~~ 260 (518)
..++|.+..|+.+++..++++.+++..+.+.++....+......+.. .+++.|+.. +|+.....
T Consensus 5 ~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 84 (342)
T COG0568 5 RLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP 84 (342)
T ss_pred ccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence 45789999999999999999999999999999888877666667665 666777764 33333222
Q ss_pred CH-HHHH-HHHHH--cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHH
Q 010092 261 SA-AQVK-KCLEV--GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLF 336 (518)
Q Consensus 261 s~-~~L~-~~~~g--d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~ 336 (518)
++ ..+. ++..| +..|+++||.+||+||++||++|. ++|++|.||||||+||||+||++|||++||+|||||+|
T Consensus 85 ~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~---~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~w 161 (342)
T COG0568 85 EEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYT---GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATW 161 (342)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhh---cCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHH
Confidence 22 2233 34456 678999999999999999999999 89999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccC
Q 010092 337 WIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLH 415 (518)
Q Consensus 337 wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD 415 (518)
||||+|.++|. +.++||+|+|+.+ ..++++++.+.+.+++|++|+++|||+.+|+++++|+.++..+..++|||
T Consensus 162 WIrqaI~raI~~q~rtIRipvh~~e-----~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd 236 (342)
T COG0568 162 WIRQAITRAIADQARTIRIPVHQVE-----LINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLD 236 (342)
T ss_pred HHHHHHHHHHHHhcchhhHhHHHHH-----HHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccC
Confidence 99999999999 9999999999999 99999999999999999999999999999999999999999999999999
Q ss_pred CCcCCchh-hhhcccccCCCCcchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHH
Q 010092 416 SRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMV 493 (518)
Q Consensus 416 ~~~~~~~e-el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerV 493 (518)
.+++++++ .+.+.+.|+...+|++.+....+.+.+...|.. |+|+|+.||++||||+|+++.|++|||+.+|||+++|
T Consensus 237 ~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERv 316 (342)
T COG0568 237 TPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERV 316 (342)
T ss_pred CcCCCCcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHH
Confidence 99987765 477888888887899999999999999999999 9999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHh-CcchhhhhhhhcC
Q 010092 494 RKHEVKGLMKLK-HPTRVDYLRQHMV 518 (518)
Q Consensus 494 Rqie~rALkKLR-~~~~~~~L~~y~~ 518 (518)
|||+.+|++||| ++.+...++.|+.
T Consensus 317 RQIE~kAl~KLr~~~~~~~~~~~~l~ 342 (342)
T COG0568 317 RQIEAKALRKLRRHPERSALLRSYLD 342 (342)
T ss_pred HHHHHHHHHHHHHhhhhhhHHHHhhC
Confidence 999999999999 7777777888863
No 7
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=100.00 E-value=1e-57 Score=491.32 Aligned_cols=303 Identities=32% Similarity=0.478 Sum_probs=270.4
Q ss_pred hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHH
Q 010092 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA 274 (518)
Q Consensus 195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~ 274 (518)
..+...|.+..||++|+.+|+||++||..|++.++.+..+++. +.. ..+|+.. ....+++.+..+..
T Consensus 205 ~~~~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~ 271 (509)
T PRK05901 205 KLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKR 271 (509)
T ss_pred hccccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHH
Confidence 3466779999999999999999999999999999866433221 111 1123221 34557777888899
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (518)
Q Consensus 275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR 353 (518)
|+++||.+|+|||+++|++|. ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|. +.++||
T Consensus 272 Ar~~LI~sNLrLVvsIAkrY~---~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IR 348 (509)
T PRK05901 272 AKNHLLEANLRLVVSLAKRYT---NRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIR 348 (509)
T ss_pred HHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCcee
Confidence 999999999999999999998 7899999999999999999999999999999999999999999999999 899999
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDV 432 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~ 432 (518)
+|.|+.+ .++++.++..+|.+.+||.||.+|||+.||+++++|..++.....++|||.+++.+++ .+.+.+.++
T Consensus 349 vP~~~~e-----~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~ 423 (509)
T PRK05901 349 IPVHMVE-----TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDS 423 (509)
T ss_pred cCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCC
Confidence 9999999 9999999999999999999999999999999999999999999999999999765544 466677777
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
....|++.+....+...|..+|..|+++|+.||.+||||++++++|+.|||+.||||+++||||+.+||.|||++.+...
T Consensus 424 ~~~~p~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~ 503 (509)
T PRK05901 424 EAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQV 503 (509)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66678888888889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhcC
Q 010092 513 LRQHMV 518 (518)
Q Consensus 513 L~~y~~ 518 (518)
|+.|+.
T Consensus 504 l~~~l~ 509 (509)
T PRK05901 504 LRDFLD 509 (509)
T ss_pred HHHhhC
Confidence 999973
No 8
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=100.00 E-value=5.2e-56 Score=457.89 Aligned_cols=299 Identities=31% Similarity=0.438 Sum_probs=264.8
Q ss_pred CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (518)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e 277 (518)
...|.+..||++|+.+|+||++||..|++.++.+..++.. |...+|+... ....+...+..|..|++
T Consensus 23 ~~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~ 89 (324)
T PRK07921 23 PAADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR 89 (324)
T ss_pred CCCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence 3458899999999999999999999999999866544332 1112221110 23456777788899999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
+||.+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.
T Consensus 90 ~Lv~~~~~lV~~iA~r~~---~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~ 166 (324)
T PRK07921 90 HLLEANLRLVVSLAKRYT---GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 166 (324)
T ss_pred HHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCH
Confidence 999999999999999999 7899999999999999999999999999999999999999999999999 889999999
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~ 435 (518)
|+.+ .+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++...
T Consensus 167 ~~~~-----~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~ 241 (324)
T PRK07921 167 HLVE-----QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEAT 241 (324)
T ss_pred HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCC
Confidence 9998 9999999999999999999999999999999999999999988899999999765544 456666665556
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 515 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~ 515 (518)
+|++.+....+...|..+|+.|+++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||.......|..
T Consensus 242 ~pe~~~~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~ 321 (324)
T PRK07921 242 SAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS 321 (324)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 67777788888999999999999999999999999998899999999999999999999999999999999999999998
Q ss_pred hc
Q 010092 516 HM 517 (518)
Q Consensus 516 y~ 517 (518)
|+
T Consensus 322 ~~ 323 (324)
T PRK07921 322 YA 323 (324)
T ss_pred hh
Confidence 86
No 9
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=7.4e-54 Score=449.29 Aligned_cols=273 Identities=34% Similarity=0.557 Sum_probs=255.3
Q ss_pred cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHH
Q 010092 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276 (518)
Q Consensus 197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~ 276 (518)
....|++.+||++|+.+|+||++||..|++.+ ..||..|+
T Consensus 92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~----------------------------------------~~Gd~~A~ 131 (367)
T PRK09210 92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRI----------------------------------------EEGDEEAK 131 (367)
T ss_pred cccCcHHHHHHHHhhccCCCCHHHHHHHHHHH----------------------------------------HhhHHHHH
Confidence 44579999999999999999999999887655 35788999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (518)
Q Consensus 277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP 355 (518)
+.||..|+++|+++|++|. +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|+ +.+++|+|
T Consensus 132 ~~Li~~~~~lV~~iA~~~~---~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip 208 (367)
T PRK09210 132 QRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP 208 (367)
T ss_pred HHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceecc
Confidence 9999999999999999999 7899999999999999999999999999999999999999999999999 89999999
Q ss_pred ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCC
Q 010092 356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDG 434 (518)
Q Consensus 356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~ 434 (518)
.|+.+ .++++.++.+.|..++||.||.+|||+.||+++++|+.++.....++|||.+.+.+++ .+.+.+.++..
T Consensus 209 ~~~~~-----~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~ 283 (367)
T PRK09210 209 VHMVE-----TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDA 283 (367)
T ss_pred HHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCC
Confidence 99999 9999999999999999999999999999999999999999999899999999865543 46667777766
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~ 514 (518)
.+|++.+....++..|..+|..||++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||++.+...|+
T Consensus 284 ~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~ 363 (367)
T PRK09210 284 TSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLK 363 (367)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHH
Confidence 77888888889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhc
Q 010092 515 QHM 517 (518)
Q Consensus 515 ~y~ 517 (518)
.|+
T Consensus 364 ~~~ 366 (367)
T PRK09210 364 DFL 366 (367)
T ss_pred Hhh
Confidence 986
No 10
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=100.00 E-value=1.6e-50 Score=449.75 Aligned_cols=242 Identities=35% Similarity=0.572 Sum_probs=226.4
Q ss_pred HHHHc---HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 268 CLEVG---RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 268 ~~~gd---~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+..|+ ..|+++||.+|+|||+++|++|. ++|++++||||||+|||++|+++|||++|++|||||+||||++|.+
T Consensus 371 i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~---~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~ 447 (619)
T PRK05658 371 ISKGEAKARRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 447 (619)
T ss_pred HhccchhhhHHHHHHHHHHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHH
Confidence 34564 47899999999999999999998 7899999999999999999999999999999999999999999999
Q ss_pred HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+|+ +.++||+|+|+.+ ..++++++...+.+++||.||++|||+.||+++++|+.++.....++|||.+++++++
T Consensus 448 ~i~~~~r~irip~~~~~-----~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~ 522 (619)
T PRK05658 448 SIADQARTIRIPVHMIE-----TINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDED 522 (619)
T ss_pred HHHHcCCceecCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCC
Confidence 999 8899999999999 9999999999999999999999999999999999999999999999999999765554
Q ss_pred -hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 424 -EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 424 -el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.+.+.+.+....+|++.+....++..|..+|+.||++|+.||.+||||+++.++|++|||+.||||+++||||+.+||+
T Consensus 523 ~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~ 602 (619)
T PRK05658 523 SHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602 (619)
T ss_pred CchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4667777766667888888888999999999999999999999999999889999999999999999999999999999
Q ss_pred HHhCcchhhhhhhhc
Q 010092 503 KLKHPTRVDYLRQHM 517 (518)
Q Consensus 503 KLR~~~~~~~L~~y~ 517 (518)
|||++.+...|+.|+
T Consensus 603 kLr~~~~~~~l~~~~ 617 (619)
T PRK05658 603 KLRHPSRSRKLRSFL 617 (619)
T ss_pred HHhchHHHHHHHHHh
Confidence 999999999999997
No 11
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=100.00 E-value=1.2e-46 Score=372.64 Aligned_cols=235 Identities=34% Similarity=0.570 Sum_probs=218.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (518)
Q Consensus 275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR 353 (518)
|+++||.+|+++|+++|++|. +++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++. +.+.++
T Consensus 1 a~~~Li~~~~~lv~~ia~~~~---~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vr 77 (238)
T TIGR02393 1 AKKQLVESNLRLVVSIAKKYT---NRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIR 77 (238)
T ss_pred CHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEE
Confidence 578999999999999999998 7899999999999999999999999999999999999999999999999 889999
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDV 432 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~ 432 (518)
+|.++.+ .++++.++...+..++|+.||.+|||+.+|+++++|..++......+|||.+.+.+++ .+.+.+.++
T Consensus 78 ip~~~~~-----~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~ 152 (238)
T TIGR02393 78 IPVHMVE-----TINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDT 152 (238)
T ss_pred eCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCC
Confidence 9999888 9999999999999999999999999999999999999999888889999998765544 355666666
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
...+|++......+...|..+|+.||++|+.||.++|||++++++|++|||+.||||.++|+|++.+|++|||+....+.
T Consensus 153 ~~~~p~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~ 232 (238)
T TIGR02393 153 SIESPDDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK 232 (238)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhH
Confidence 65667777778888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhc
Q 010092 513 LRQHM 517 (518)
Q Consensus 513 L~~y~ 517 (518)
|+.|+
T Consensus 233 ~~~~~ 237 (238)
T TIGR02393 233 LKSFL 237 (238)
T ss_pred HHHhh
Confidence 99886
No 12
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=100.00 E-value=5.3e-44 Score=369.21 Aligned_cols=270 Identities=29% Similarity=0.443 Sum_probs=244.0
Q ss_pred cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHH
Q 010092 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276 (518)
Q Consensus 197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~ 276 (518)
....|.+++|+++|+..|+||+++|..|...+ ..||..|+
T Consensus 49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~----------------------------------------~~Gd~~A~ 88 (325)
T PRK05657 49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRA----------------------------------------LRGDFAAR 88 (325)
T ss_pred cccccHHHHHHHHHhcCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHH
Confidence 35789999999999999999999998885544 56889999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (518)
Q Consensus 277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP 355 (518)
+.||..|.++|+++|++|. +++.+++||+||||+|||+++++||+.+|++|+|||+||||++|.+++. +.+.+++|
T Consensus 89 ~~Li~~y~~~V~~~a~~~~---~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p 165 (325)
T PRK05657 89 QRMIESNLRLVVKIAKRYL---NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLP 165 (325)
T ss_pred HHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccC
Confidence 9999999999999999998 7889999999999999999999999999999999999999999999998 88999999
Q ss_pred ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCC
Q 010092 356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDG 434 (518)
Q Consensus 356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~ 434 (518)
.++.. .++.+.++...|...+|+.||.+|||+.+|+++++|..++.......|||.+...+.. .+.+.+.+...
T Consensus 166 ~~~~~-----~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~ 240 (325)
T PRK05657 166 VHVVK-----ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQE 240 (325)
T ss_pred HHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCC
Confidence 99877 7888888889999999999999999999999999999999988889999988654433 34555665555
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~ 514 (518)
.+|++.+...++...|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+....+.
T Consensus 241 ~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~ 320 (325)
T PRK05657 241 NGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS 320 (325)
T ss_pred CCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence 56777788888889999999999999999999999999999999999999999999999999999999999877665554
No 13
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.8e-43 Score=359.96 Aligned_cols=267 Identities=25% Similarity=0.270 Sum_probs=221.2
Q ss_pred CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (518)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e 277 (518)
...++++.|++++..+|+||+++|..|++.++ ..||..|++
T Consensus 3 ~~~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~---------------------------------------~~gd~~A~~ 43 (289)
T PRK07500 3 ADASADRSMIRSAMKAPYLEREEEHALAYRWK---------------------------------------DHRDEDALH 43 (289)
T ss_pred cchhHHHHHHHHHhcCCCCCHHHHHHHHHHHH---------------------------------------HCCCHHHHH
Confidence 45688999999999999999999998876541 247899999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
.||..|+++|+++|++|. +++.+++||+||||+|||+|+++|||.+|.+|+|||+||||++|.++++ +.+++|+|.
T Consensus 44 ~Lv~~~~~lV~~~a~~~~---~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~ 120 (289)
T PRK07500 44 RIISAHMRLVISMAGKFR---RFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGT 120 (289)
T ss_pred HHHHHhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCc
Confidence 999999999999999998 7899999999999999999999999999999999999999999999999 778999999
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCccccCCCcCCchh---hhhcccccC
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQE---EFINGITDV 432 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~-~~~~~~SLD~~~~~~~e---el~~~l~d~ 432 (518)
+.....++..+.+++.....+...+|+.||.+|||+.||+++++|..+.. ....++|||.+.+++++ .+.+.+.++
T Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~ 200 (289)
T PRK07500 121 SSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD 200 (289)
T ss_pred cHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC
Confidence 86542222233333333333344789999999999999999999988753 45679999998765443 355556554
Q ss_pred CCCcchhhhH----HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 433 DGVENENQRQ----PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 433 ~~~~~ee~~~----~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
. .+|++.+. ...+...|..+|+.||++|+.||.++||. .+++|++|||+.||||+++|+|++++|+++||...
T Consensus 201 ~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 201 S-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred C-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3 34554433 23456789999999999999999999952 47899999999999999999999999999999765
Q ss_pred h
Q 010092 509 R 509 (518)
Q Consensus 509 ~ 509 (518)
.
T Consensus 278 ~ 278 (289)
T PRK07500 278 L 278 (289)
T ss_pred H
Confidence 4
No 14
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=100.00 E-value=1.7e-43 Score=359.19 Aligned_cols=261 Identities=23% Similarity=0.283 Sum_probs=214.8
Q ss_pred CcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHH
Q 010092 199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278 (518)
Q Consensus 199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~ 278 (518)
+.+.+..|++++...|+||.++|..|+... ...||..|++.
T Consensus 12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~Gd~~a~~~ 52 (284)
T PRK06596 12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRL---------------------------------------REHGDLEAAKQ 52 (284)
T ss_pred CccHHHHHHHHHhccCCCCHHHHHHHHHHH---------------------------------------HHcCCHHHHHH
Confidence 448899999999999999999998886643 13588999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG 357 (518)
Q Consensus 279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~ 357 (518)
||.+|+++|+++|++|. +.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++ +.++|++|.+
T Consensus 53 Lv~~~~~lV~~ia~~~~---~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~ 129 (284)
T PRK06596 53 LVLSHLRFVVHIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATT 129 (284)
T ss_pred HHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccch
Confidence 99999999999999998 7899999999999999999999999999999999999999999999999 6567899986
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCCcCCchh---hhhcccccCC
Q 010092 358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVD 433 (518)
Q Consensus 358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~-~~~~~SLD~~~~~~~e---el~~~l~d~~ 433 (518)
.... ....++.+...++. .+++||.+|||+.||+++++|..++.. ....+|||.+.+++++ ++.+.+.+.
T Consensus 130 ~~~~---~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~- 203 (284)
T PRK06596 130 KAQR---KLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK- 203 (284)
T ss_pred HHHH---HHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-
Confidence 4320 02233333333332 349999999999999999999998763 4578999998754422 245555554
Q ss_pred CCcchhhhHHH----HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 434 GVENENQRQPA----LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 434 ~~~~ee~~~~~----~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..+|++.++.. .+...|..+|+.||++|+.||.+|||.+ +++|++|||+.||||+++|+|++.+|++|||+...
T Consensus 204 ~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~ 281 (284)
T PRK06596 204 SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIE 281 (284)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33455544432 4678899999999999999999999642 68999999999999999999999999999997654
No 15
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=100.00 E-value=1.9e-42 Score=349.05 Aligned_cols=257 Identities=25% Similarity=0.311 Sum_probs=208.8
Q ss_pred hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHH
Q 010092 202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK 281 (518)
Q Consensus 202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~ 281 (518)
.+..|+++|+.+|+|++++|..|+..+ ...||..|++.||.
T Consensus 2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~gd~~a~~~Lv~ 42 (270)
T TIGR02392 2 SLDAYIRAVNRIPMLTPEEEYQLAKRL---------------------------------------REHGDLDAAKKLVL 42 (270)
T ss_pred hHHHHHHHHhcCCCCCHHHHHHHHHHH---------------------------------------HHCCCHHHHHHHHH
Confidence 467899999999999999998886653 13588999999999
Q ss_pred HHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccccccc
Q 010092 282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLES 360 (518)
Q Consensus 282 ~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e 360 (518)
+|+++|+++|++|. +++.+++||+|||++|||+|+++|||++|++|+|||+|||+++|.++++ +.+++|+|.+...
T Consensus 43 ~~~~lV~~~a~~~~---~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~ 119 (270)
T TIGR02392 43 SHLRFVVKIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQ 119 (270)
T ss_pred HhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHH
Confidence 99999999999998 7899999999999999999999999999999999999999999999999 6567899976332
Q ss_pred hhhHHHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHHh-cCCccccCCCcCCchh---hhhcccccCCCC
Q 010092 361 TSIMQVRGEIQRAKLELLFELKRVP-TDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGV 435 (518)
Q Consensus 361 ~~~~~~~~ki~ka~~eL~~elgR~P-T~eELA~~lgis~e~v~~~l~~-~~~~~SLD~~~~~~~e---el~~~l~d~~~~ 435 (518)
.+...++.+....+. .++.| +.+|||+.||+++++|..++.. ....+|||.+.+++++ .+.+.+.++. .
T Consensus 120 ---~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~ 193 (270)
T TIGR02392 120 ---RKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-S 193 (270)
T ss_pred ---HHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-C
Confidence 113334444443332 22566 6999999999999999998653 3458999998755432 2444555543 3
Q ss_pred cchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 436 ENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 436 ~~ee~~~~----~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
+|++.+.. ..+...|..+|..||++|+.||.++||. .+++|++|||+.||||+++|+|++.+||+|||..+
T Consensus 194 ~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 194 DPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 45554433 3467889999999999999999999963 35899999999999999999999999999999754
No 16
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=1.2e-42 Score=349.53 Aligned_cols=221 Identities=24% Similarity=0.306 Sum_probs=194.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCC
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF 351 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~ 351 (518)
..++++||.+|++||+++|++|. ++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++ +.++
T Consensus 39 ~~~r~~Lv~~~l~LV~~iA~~y~---~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ 115 (264)
T PRK07122 39 QRQRDRIVTRCLPLADHIARRFD---GRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWS 115 (264)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCc
Confidence 45899999999999999999998 6799999999999999999999999999999999999999999999999 7889
Q ss_pred ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhhhhccc
Q 010092 352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGI 429 (518)
Q Consensus 352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~eel~~~l 429 (518)
||+|.++.+ ..++++++..+|.+++|+.||.+|||+.||+++++|..++.. ...++|||.+.+.+++.. ..+
T Consensus 116 ir~Pr~~~~-----~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~-~~~ 189 (264)
T PRK07122 116 VKVPRRLKE-----LHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDA-RAI 189 (264)
T ss_pred cccCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCc-ccc
Confidence 999999998 999999999999999999999999999999999999998865 457899999875432210 111
Q ss_pred ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.+. ..+++..++.......|..+|+.||++|+.||.++| .+++|++|||+.||+|.++|++++++|+++||..
T Consensus 190 ~d~-~~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 190 ADT-LGDVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred hhc-cCCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 111 122344456667788899999999999999999999 4899999999999999999999999999999975
No 17
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=100.00 E-value=3.5e-40 Score=334.82 Aligned_cols=267 Identities=29% Similarity=0.433 Sum_probs=238.2
Q ss_pred CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN 277 (518)
Q Consensus 198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e 277 (518)
.-.|++++||++|..+|.||.+++..|...+ .+|+..|++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~----------------------------------------~~gd~~a~~ 49 (285)
T TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRA----------------------------------------LAGDFEARK 49 (285)
T ss_pred CcchHHHHHHHHHhccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHH
Confidence 3569999999999999999999998775544 568899999
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
.||..|.++|+++|.+|. +++.+++||+||||+|||+|+++||+..|++|+||++|||+.++++++. +.+.+++|.
T Consensus 50 ~L~~~y~~~v~~~a~~~~---~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~ 126 (285)
T TIGR02394 50 VMIESNLRLVVSIAKHYV---NRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV 126 (285)
T ss_pred HHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence 999999999999999998 7899999999999999999999999999999999999999999999999 788999999
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~ 435 (518)
++.. .++.+.+....+...+|+.|+.+++|+.+|++++++..++......+|+|.+...+.. .+.+.+.++...
T Consensus 127 ~~~~-----~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~ 201 (285)
T TIGR02394 127 HVIK-----ELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSI 201 (285)
T ss_pred HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCC
Confidence 8887 8888888877788889999999999999999999999999988889999987543332 233444444445
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
+|++.+...+....|..+|..||+++|.||.|+|||.+.+++|++|||+.||+|.++|++++++|+++||..+....
T Consensus 202 ~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~ 278 (285)
T TIGR02394 202 DPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDG 278 (285)
T ss_pred CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 67777888888999999999999999999999999998999999999999999999999999999999998765433
No 18
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=100.00 E-value=3.8e-40 Score=329.95 Aligned_cols=227 Identities=29% Similarity=0.377 Sum_probs=196.2
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT- 347 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~- 347 (518)
..|+..|+++||..|+++|+++|++|.. ..+.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++
T Consensus 20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~--~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~ 97 (256)
T PRK07408 20 QNPSIALRNQLVELNLGLVRKEAHRWSN--QCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRD 97 (256)
T ss_pred HCCCHHHHHHHHHHhHHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999999999973 2366799999999999999999999999999999999999999999999
Q ss_pred hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhh-
Q 010092 348 VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE- 424 (518)
Q Consensus 348 ~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~ee- 424 (518)
+.++||+|.++.+ ..++++++...|.+++|++||.+|||+.||+++++|..++.. ....+|||.+...+++.
T Consensus 98 ~~~~vr~pr~~~~-----~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~ 172 (256)
T PRK07408 98 KSPTVRIPRRWQE-----LQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGS 172 (256)
T ss_pred cCCeeeeCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCc
Confidence 7889999999988 999999999999999999999999999999999999998753 45688999986543332
Q ss_pred --hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 425 --FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 425 --l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+.+.+.++... +. ....+....|..+|..||++++.||.++| ++++|++|||+.||+|.++|++++.+|++
T Consensus 173 ~~l~d~~~d~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~ 245 (256)
T PRK07408 173 TSLGDLLPDPRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLD 245 (256)
T ss_pred cccccccCCcccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 23333332211 11 12335567799999999999999999999 48999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||..+.
T Consensus 246 kLr~~l~ 252 (256)
T PRK07408 246 QLKKLLQ 252 (256)
T ss_pred HHHHHhh
Confidence 9997654
No 19
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=100.00 E-value=5.8e-39 Score=320.72 Aligned_cols=241 Identities=27% Similarity=0.353 Sum_probs=209.7
Q ss_pred cCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHH
Q 010092 210 MKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF 289 (518)
Q Consensus 210 i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~s 289 (518)
...+|+||++||..|+..+ ..||..|++.|+..|+++|++
T Consensus 10 ~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~~~~~v~~ 49 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRM----------------------------------------QSGDTTAREKLINGNLRLVLS 49 (254)
T ss_pred ccCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHHHH
Confidence 4678999999887775443 357889999999999999999
Q ss_pred HHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHH
Q 010092 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGE 369 (518)
Q Consensus 290 iAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~k 369 (518)
+|++|. +++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.+++++.+.+|+|.++.+ ..++
T Consensus 50 ~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~-----~~~~ 121 (254)
T TIGR02850 50 VIQRFN---NRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRD-----IAYK 121 (254)
T ss_pred HHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHH-----HHHH
Confidence 999998 77899999999999999999999999999999999999999999999996668999999888 8889
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh---hhhcccccCCCCcchhhhHHHHH
Q 010092 370 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFINGITDVDGVENENQRQPALL 446 (518)
Q Consensus 370 i~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e---el~~~l~d~~~~~~ee~~~~~~l 446 (518)
+.++...+..++|+.||.+|||+.||+++++|..++.....+.|||.+..++++ .+.+.+.++.. +. .....
T Consensus 122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~--~~---~~~~~ 196 (254)
T TIGR02850 122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN--KD---SQWLE 196 (254)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--cH---HHHHh
Confidence 999999999999999999999999999999999999998889999988643332 23444444322 11 22345
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 447 ~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
...|..+|+.|+++++.||.++| .+++|++|||+.||+|.++|++++.+|+++||+.
T Consensus 197 ~~~l~~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 197 GIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 56799999999999999999999 4789999999999999999999999999999964
No 20
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=100.00 E-value=2.7e-39 Score=324.05 Aligned_cols=228 Identities=26% Similarity=0.355 Sum_probs=198.8
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
.|+..|+++||..|+++|+++|++|...+..+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++..
T Consensus 19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~ 98 (257)
T PRK05911 19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ 98 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence 57889999999999999999999986433456789999999999999999999999999999999999999999999933
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCCcCC--chh--
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGV--TQE-- 423 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLD~~~~~--~~e-- 423 (518)
. ++|.++.+ ..+++..+...|.+.+|+.||.+|||+.+|+++++|..++.... .++|||.+... +++
T Consensus 99 ~--~~pr~~~~-----~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~ 171 (257)
T PRK05911 99 D--WVPRSVHQ-----KANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAG 171 (257)
T ss_pred C--CCCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccc
Confidence 2 38998888 89999999999999999999999999999999999999987654 46899987532 111
Q ss_pred -hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 424 -EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 424 -el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.+.+.+.++....|++.....++...|..+|..||++|+.||.++| ++++|++|||+.||+|.++|++++.+|++
T Consensus 172 ~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 172 LALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred cchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 2445555555455667777778888999999999999999999999 48999999999999999999999999999
Q ss_pred HHhCcc
Q 010092 503 KLKHPT 508 (518)
Q Consensus 503 KLR~~~ 508 (518)
+||+.+
T Consensus 248 kLr~~l 253 (257)
T PRK05911 248 KLRATL 253 (257)
T ss_pred HHHHHH
Confidence 999754
No 21
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=100.00 E-value=3.9e-38 Score=312.02 Aligned_cols=226 Identities=32% Similarity=0.428 Sum_probs=198.6
Q ss_pred HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC-CHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~-~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
....|+..++ .||+.|+|||.++|++|. +++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.++
T Consensus 17 ~~~~g~~~~~-~Li~~ylpLV~~ia~k~~---~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~ 92 (247)
T COG1191 17 YYAEGDEEAR-RLIERYLPLVKSIARKFE---NRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY 92 (247)
T ss_pred HHHhcCHHHH-HHHHHHHHHHHHHHHHHH---hcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence 3456889999 999999999999999999 4555 9999999999999999999999999999999999999999999
Q ss_pred HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCCcCCchh
Q 010092 346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQE 423 (518)
Q Consensus 346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLD~~~~~~~e 423 (518)
++....+++|..+.+ ..+++..+..+|..++||+||++|||+.||++.++|..++.... ..+|+|.....+++
T Consensus 93 LR~~~~v~vpR~~~~-----~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d 167 (247)
T COG1191 93 LRKNDSVKVPRSLRE-----LGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD 167 (247)
T ss_pred HHhCCCccCcHHHHH-----HHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence 994449999998888 99999999999999999999999999999999999999998764 77888876543332
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
.. .++...++++.++..++...|.+++..|+++|+.||.+|| ++++|++|||+.||||+++|+|++.+|+++
T Consensus 168 ~~----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~k 239 (247)
T COG1191 168 DD----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKK 239 (247)
T ss_pred cc----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 21 2222334566677788888888898999999999999999 689999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
||+.+.
T Consensus 240 Lr~~l~ 245 (247)
T COG1191 240 LRKELN 245 (247)
T ss_pred HHHHhc
Confidence 997643
No 22
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=100.00 E-value=1.9e-37 Score=310.33 Aligned_cols=222 Identities=28% Similarity=0.377 Sum_probs=194.7
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
..||..|++.||..|+++|+++|++|. +++.+++||+|||++|||+|+++||+.+|.+|+||++|||+++|.++++.
T Consensus 32 ~~gd~~a~~~l~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~ 108 (258)
T PRK08215 32 QNGDKEAREKLINGNLRLVLSVIQRFN---NRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRD 108 (258)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence 357889999999999999999999998 78899999999999999999999999999999999999999999999996
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh---h
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---F 425 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee---l 425 (518)
.+.+++|.++.. ...++.++..++..++|+.|+++|||+.+|+++++|..++.....+.|||.+...+++. +
T Consensus 109 ~~~vrip~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 183 (258)
T PRK08215 109 NNPIRVSRSLRD-----IAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYV 183 (258)
T ss_pred CCceEecHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhh
Confidence 678899998887 88889999999999999999999999999999999999998888888999886543322 2
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+.+.++.. ..........|..+|+.||++++.||.++| ++++|+.|||+.||+|.++|++++++|+++||
T Consensus 184 ~~~~~~~~~-----~~~~~~~~~~l~~~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 184 MDQISDEKN-----KDENWLEEIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred hhhccCccc-----cHHHHHhHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 333333221 122334556789999999999999999999 47899999999999999999999999999999
Q ss_pred Cc
Q 010092 506 HP 507 (518)
Q Consensus 506 ~~ 507 (518)
+.
T Consensus 255 ~~ 256 (258)
T PRK08215 255 KY 256 (258)
T ss_pred HH
Confidence 64
No 23
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=100.00 E-value=3.5e-36 Score=302.92 Aligned_cols=249 Identities=23% Similarity=0.352 Sum_probs=213.7
Q ss_pred CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHH
Q 010092 211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV 290 (518)
Q Consensus 211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~si 290 (518)
+.+|+||+++|..|+..++ ..||..|++.|+..|+++|+.+
T Consensus 7 ~~~~~~~~~~e~~l~~~~~---------------------------------------~~~d~~a~~~l~~~y~~lv~~~ 47 (268)
T PRK06288 7 GKIPKYAQQDETELWREYK---------------------------------------KTGDPKIREYLILKYSPLVKYV 47 (268)
T ss_pred CCCccccchHHHHHHHHHH---------------------------------------HcCCHHHHHHHHHHHHHHHHHH
Confidence 6789999999998876652 3468899999999999999999
Q ss_pred HHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHHH
Q 010092 291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEI 370 (518)
Q Consensus 291 Akky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~ki 370 (518)
|++|......+.+++||+||||+|||+|+++||+.+|++|+||++|||++.|.++++. .+++|.++.. ..+++
T Consensus 48 a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~--~~~~p~~~~~-----~~~~i 120 (268)
T PRK06288 48 AGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRS--IDWIPRSVRQ-----KARQI 120 (268)
T ss_pred HHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh--cCccCHHHHH-----HHHHH
Confidence 9998622235778999999999999999999999999999999999999999999983 3468888776 88899
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchh----hhhcccccCCCCcchhhhHHH
Q 010092 371 QRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQE----EFINGITDVDGVENENQRQPA 444 (518)
Q Consensus 371 ~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~e----el~~~l~d~~~~~~ee~~~~~ 444 (518)
+++...|.+++|+.||.+|||+.+|++.+++..++... ...+|||.....+++ ++.+.+.++...+|++.+...
T Consensus 121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~ 200 (268)
T PRK06288 121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAERE 200 (268)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHH
Confidence 99999999999999999999999999999999998753 467899887531111 244555555556677777888
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
+....|..+|..||++++.||.++| .+++|++|||+.||+|.++|++++.+|+++||....
T Consensus 201 e~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~ 261 (268)
T PRK06288 201 EIKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261 (268)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 8889999999999999999999999 589999999999999999999999999999998654
No 24
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=100.00 E-value=3.9e-36 Score=295.56 Aligned_cols=224 Identities=30% Similarity=0.398 Sum_probs=196.9
Q ss_pred HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (518)
Q Consensus 267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI 346 (518)
+...||..|++.|+..|.++|+++|++|. +++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.+++
T Consensus 4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~l 80 (231)
T TIGR02885 4 LAQNGDKEARDKLIECNLRLVWSIVKRFL---NRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL 80 (231)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 34578999999999999999999999998 788999999999999999999999999999999999999999999999
Q ss_pred HhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh---
Q 010092 347 TVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE--- 423 (518)
Q Consensus 347 ~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e--- 423 (518)
+....+++|.++.. ...++.++...+..++|+.||.+|||+.+|++++++..++.......|||.+...+++
T Consensus 81 r~~~~i~~p~~~~~-----~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~ 155 (231)
T TIGR02885 81 RDDGIIKVSRSLKE-----LARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPI 155 (231)
T ss_pred HhCCCeECCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcc
Confidence 95568999999888 9999999999999999999999999999999999999999888888999987654432
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
.+++.+.++.. + .........|..+|+.||++|+.||.++|+ +++|++|||+.||+|+++|++++++|+++
T Consensus 156 ~~~d~~~~~~~--~---~~~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~ 226 (231)
T TIGR02885 156 YLLDQIADKGS--E---DSDWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKK 226 (231)
T ss_pred hhhhhcCCCCc--c---HHhHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 23344433321 1 122345668899999999999999999994 78999999999999999999999999999
Q ss_pred HhCc
Q 010092 504 LKHP 507 (518)
Q Consensus 504 LR~~ 507 (518)
||..
T Consensus 227 Lr~~ 230 (231)
T TIGR02885 227 MKEK 230 (231)
T ss_pred HHHh
Confidence 9964
No 25
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=100.00 E-value=3e-35 Score=293.76 Aligned_cols=225 Identities=25% Similarity=0.301 Sum_probs=196.9
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hc
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VS 349 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~s 349 (518)
||..|+++|+..|.++|+.+|++|. +++.+++||+||||+|||+|+++||++.|.+|+||+++||++.|.++++ +.
T Consensus 26 gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~ 102 (255)
T TIGR02941 26 QNGEAQEKLVDHYQNLVYSIAYKYS---KGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKT 102 (255)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcC
Confidence 6789999999999999999999998 7899999999999999999999999999999999999999999999999 67
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhhc
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFIN 427 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~~ 427 (518)
+.+++|.++.+ ..++++++...+...+|+.||.+|||+.+|++.+++..++... ....|||.++..+++.-..
T Consensus 103 ~~iri~~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~ 177 (255)
T TIGR02941 103 WSVHVPRRIKE-----LGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTV 177 (255)
T ss_pred CCcCCCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCccc
Confidence 78999998888 8999999999999999999999999999999999999988754 4678999886544332111
Q ss_pred ccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 428 ~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
...+. ..++++.....+....|..+|+.||+++|.||.++| .+++|++|||+.||+|.++|++++++|+++||..
T Consensus 178 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 178 ARLDS-VGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred ccccc-cCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 11111 122455566677778899999999999999999999 5899999999999999999999999999999974
Q ss_pred c
Q 010092 508 T 508 (518)
Q Consensus 508 ~ 508 (518)
+
T Consensus 253 ~ 253 (255)
T TIGR02941 253 A 253 (255)
T ss_pred h
Confidence 3
No 26
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=100.00 E-value=7.2e-35 Score=285.67 Aligned_cols=222 Identities=31% Similarity=0.396 Sum_probs=193.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcC
Q 010092 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSS 350 (518)
Q Consensus 272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr 350 (518)
|..|++.||..|.++|+++|++|. +++.+++||+|||++|||+|+++||+++|.+|+||++|||++.|.++++ +.+
T Consensus 1 ~~~a~~~lv~~y~~~v~~~a~~~~---~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~ 77 (227)
T TIGR02980 1 DKEAREKLVELNLPLVRSIARRFR---NRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTW 77 (227)
T ss_pred CHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence 467999999999999999999998 7788999999999999999999999999999999999999999999999 667
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--ccccCCCcCCchhhhhcc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSLHSRHGVTQEEFING 428 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~--~~SLD~~~~~~~eel~~~ 428 (518)
.+++|.++.+ ..++++++...+...+|+.|+.+|||+.+|++.+++..++..... ..|||.+..++++. ...
T Consensus 78 ~~ri~~~~~~-----~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~-~~~ 151 (227)
T TIGR02980 78 AVRVPRRLKE-----LGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGD-PIA 151 (227)
T ss_pred ceecCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCC-Ccc
Confidence 9999998888 889999999999999999999999999999999999999887654 89999886522211 111
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
+.+ ...+++...+..+....|..+|..||++++.||.++| .+++|++|||+.||+|.++|++++++|+++||..
T Consensus 152 ~~d-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 152 LLD-TLGDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred ccc-ccCCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 111 1112344455567778899999999999999999999 4799999999999999999999999999999964
No 27
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=100.00 E-value=6.9e-34 Score=283.55 Aligned_cols=229 Identities=25% Similarity=0.330 Sum_probs=197.3
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
..||..|++.||..|.++|+++|.+|..++.++.+.+||+||||+|||+++++||+.+|.+|+||++|||++.|.++++.
T Consensus 17 ~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~ 96 (251)
T PRK07670 17 EERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRK 96 (251)
T ss_pred HcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh
Confidence 35689999999999999999999999743346889999999999999999999999999999999999999999999994
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhh--
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE-- 424 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~ee-- 424 (518)
.. ++|.++.+ .+++++++...+.+.+|+.|+.+|||+.+|++.++|..++.. ....+|||.+...+++.
T Consensus 97 ~~--~~p~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~ 169 (251)
T PRK07670 97 ED--WLPRSMRE-----KTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN 169 (251)
T ss_pred cC--CCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcch
Confidence 32 58887777 888999999999999999999999999999999999999864 56789999886433332
Q ss_pred hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
+...+.++...++++.....+....|..+|+.||+++|.||.++| .+++|++|||+.||+|.++|++++.+|+++|
T Consensus 170 ~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~L 245 (251)
T PRK07670 170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKL 245 (251)
T ss_pred hhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 222333444445666667777788899999999999999999999 5899999999999999999999999999999
Q ss_pred hCcc
Q 010092 505 KHPT 508 (518)
Q Consensus 505 R~~~ 508 (518)
|...
T Consensus 246 r~~l 249 (251)
T PRK07670 246 KKLL 249 (251)
T ss_pred HHHh
Confidence 9753
No 28
>PRK05572 sporulation sigma factor SigF; Validated
Probab=100.00 E-value=1.2e-33 Score=281.93 Aligned_cols=221 Identities=29% Similarity=0.413 Sum_probs=193.5
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
..|+..|++.|+..|.++|+.+|++|. +++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.++++.
T Consensus 27 ~~gd~~a~~~L~~~y~~~v~~~a~~~~---~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~ 103 (252)
T PRK05572 27 QDGDQEARDTLVEKNLRLVWSVVQRFL---NRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD 103 (252)
T ss_pred HcCCHHHHHHHHHHhHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHh
Confidence 457889999999999999999999998 78899999999999999999999999988899999999999999999996
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh---h
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---F 425 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee---l 425 (518)
.+.+++|.++.. ..++++++...+..++|+.|+++|+|+.+|++++++..++.......||+.+..+++.+ +
T Consensus 104 ~~~~r~~~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~ 178 (252)
T PRK05572 104 DGTVKVSRSLKE-----TANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITL 178 (252)
T ss_pred CCCCCCCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchh
Confidence 678999998888 99999999999999999999999999999999999999988888889998876433221 1
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+.+.++. .........|..+|+.||++++.||.++| .+++|++|||+.+|+|.++|++++++|+++||
T Consensus 179 ~d~~~~~~-------~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr 247 (252)
T PRK05572 179 LDQIADQS-------EEDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMK 247 (252)
T ss_pred hhhcCCCc-------hhhHHHHHHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 22222211 12234567899999999999999999999 47899999999999999999999999999999
Q ss_pred Ccc
Q 010092 506 HPT 508 (518)
Q Consensus 506 ~~~ 508 (518)
..+
T Consensus 248 ~~l 250 (252)
T PRK05572 248 EKL 250 (252)
T ss_pred HHh
Confidence 643
No 29
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=100.00 E-value=1.2e-33 Score=279.13 Aligned_cols=213 Identities=21% Similarity=0.278 Sum_probs=178.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR 353 (518)
.....|+..|+|+|..+|++|......+.+.+||+|||++|||+|+++|||..| +|+|||+||||++|.++++... .
T Consensus 15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~--~ 91 (231)
T PRK12427 15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD--W 91 (231)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC--C
Confidence 345678999999999999999855456789999999999999999999998666 8999999999999999999321 2
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhhhhccccc
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITD 431 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~eel~~~l~d 431 (518)
+|.++.. ..++++++...+.+++|+.||.+|||+.||++.++|.+++.. .....|||.+.+++++. +.+ +
T Consensus 92 ~~r~vr~-----~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~--~~~-~ 163 (231)
T PRK12427 92 RPRRLRQ-----KTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN--DIL-Q 163 (231)
T ss_pred CCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc--ccc-C
Confidence 5666655 889999999999999999999999999999999999999864 45789999986543321 111 1
Q ss_pred CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
. .+++ +.......|..+|..||++++.||.++| .+++|++|||+.||||.++|+|++.+|+++||.
T Consensus 164 ~--~~~~---~~~~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~ 229 (231)
T PRK12427 164 S--RDLE---ENIIIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS 229 (231)
T ss_pred C--CCHH---HHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 1 1122 2233566789999999999999999999 589999999999999999999999999999985
No 30
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=100.00 E-value=1e-33 Score=277.32 Aligned_cols=218 Identities=28% Similarity=0.415 Sum_probs=189.3
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccc
Q 010092 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGL 358 (518)
Q Consensus 279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~ 358 (518)
|+..|.++|+.+|++|..++.++.+++||+|||++|||+|+++|||++|++|+||+++||++.+.+++++. .++|.++
T Consensus 1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~--~~~p~~~ 78 (224)
T TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRL--DWVPRSL 78 (224)
T ss_pred CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHc--CccCHHH
Confidence 58899999999999998543478999999999999999999999999999999999999999999999842 2578776
Q ss_pred cchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCc--hhhhhcccccCCC
Q 010092 359 ESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVT--QEEFINGITDVDG 434 (518)
Q Consensus 359 ~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~--~eel~~~l~d~~~ 434 (518)
.. .++++.++..++.+.+|+.|+.+|||+.+|+++++|..++.. ....+|+|...... ...+.+.+.++..
T Consensus 79 ~~-----~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~ 153 (224)
T TIGR02479 79 RQ-----KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKS 153 (224)
T ss_pred HH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcccccc
Confidence 66 899999999999999999999999999999999999999864 34677888765432 2234444554455
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.++++.+...+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++++++|+++||..
T Consensus 154 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 154 EDPEEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 56777777888889999999999999999999999 5899999999999999999999999999999964
No 31
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=100.00 E-value=4.1e-33 Score=278.68 Aligned_cols=227 Identities=25% Similarity=0.299 Sum_probs=196.3
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-h
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V 348 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~ 348 (518)
.||..|++.||..|.++|+++|++|. +++.+++||+||||++||+++++||+..|.+|+||+++||++.|.++++ +
T Consensus 25 ~gd~~a~~~l~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~ 101 (257)
T PRK08583 25 NQDEEAQEKLVKHYKNLVESLAYKYS---KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDK 101 (257)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhc
Confidence 37899999999999999999999998 7888999999999999999999999999989999999999999999999 6
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhh
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFI 426 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~ 426 (518)
...+++|.++.+ ..++++++...+...+++.|+.+|+|+.+|++.+++..++... ...+|+|.+.+.+.+...
T Consensus 102 ~~~~~i~r~~~~-----~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~ 176 (257)
T PRK08583 102 TWSVHVPRRIKE-----LGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGST 176 (257)
T ss_pred CCCcCCCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCcc
Confidence 788999999888 8899999999999999999999999999999999998887754 367888887654333211
Q ss_pred cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
..+.+ ...++++.....+....|..+|..||++++.||.++| ++++|++|||+.||||.++|++++++|+++||.
T Consensus 177 ~~~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 177 VTLLD-IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred chHhh-hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 11111 1123455566667778899999999999999999999 489999999999999999999999999999997
Q ss_pred cch
Q 010092 507 PTR 509 (518)
Q Consensus 507 ~~~ 509 (518)
...
T Consensus 252 ~l~ 254 (257)
T PRK08583 252 AAF 254 (257)
T ss_pred Hhc
Confidence 553
No 32
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=100.00 E-value=1.6e-32 Score=271.16 Aligned_cols=226 Identities=24% Similarity=0.358 Sum_probs=191.7
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
.|.-+++.|+..|.++|+.+|.+|..+++++.+++||+||||+|||+++++|||+.|.+|+||+++||++.|.+++++..
T Consensus 5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~ 84 (236)
T PRK06986 5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD 84 (236)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence 45678999999999999999999974435788999999999999999999999999999999999999999999999432
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhhcc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~~~ 428 (518)
++|.++.. ...++.++...+.+.+|+.||.+|||+.+|++.++|..++... ...+|++...+.+++.+. .
T Consensus 85 --~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~-~ 156 (236)
T PRK06986 85 --WVPRSVRR-----NAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSIL-V 156 (236)
T ss_pred --CCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccc-c
Confidence 25665555 6677888888999999999999999999999999999998863 456788887654444332 2
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
..++...++++.+...+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++++.+|+++||+..
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 157 TEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred ccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 22233345666677777888999999999999999999999 58999999999999999999999999999999754
No 33
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=99.95 E-value=1.1e-26 Score=229.13 Aligned_cols=208 Identities=30% Similarity=0.371 Sum_probs=164.1
Q ss_pred hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHH
Q 010092 202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK 281 (518)
Q Consensus 202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~ 281 (518)
++..|+.++++.|.||+++|..|...+ ..||..|++.|+.
T Consensus 17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~----------------------------------------~~gd~~a~~~l~~ 56 (233)
T PRK05803 17 FLVSYVKNNSFPQPLSEEEERKYLELM----------------------------------------KEGDEEARNILIE 56 (233)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHH
Confidence 577899999999999999887764443 3578899999999
Q ss_pred HHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccccccccc
Q 010092 282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLES 360 (518)
Q Consensus 282 ~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~e 360 (518)
.|.++|+++|.+|. +++.+++||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++ .+..
T Consensus 57 ~y~~~l~~~a~~~~---~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~-------- 125 (233)
T PRK05803 57 RNLRLVAHIVKKFE---NTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK-------- 125 (233)
T ss_pred HhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc--------
Confidence 99999999999999 78999999999999999999999999988899999999999999998872 1110
Q ss_pred hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc--h--hhhhcccccCCCCc
Q 010092 361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT--Q--EEFINGITDVDGVE 436 (518)
Q Consensus 361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~--~--eel~~~l~d~~~~~ 436 (518)
...+++.....+ + ..+.+...+ ...+
T Consensus 126 -------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 155 (233)
T PRK05803 126 -------------------------------------------------KEVSLQDPIGVDKEGNEISLIDILGS-EEDD 155 (233)
T ss_pred -------------------------------------------------cCCCccccccCCCCcCcccHHHHccC-CCCC
Confidence 000111110000 0 011111111 1223
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
+++..........|..+|+.||+++|.||.++|++.+.+++|++|||+.||+|.++|++++++|+++||..+..
T Consensus 156 ~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~ 229 (233)
T PRK05803 156 VIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR 229 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666677789999999999999999999988777899999999999999999999999999999986543
No 34
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=99.91 E-value=4.4e-23 Score=203.31 Aligned_cols=182 Identities=25% Similarity=0.398 Sum_probs=138.5
Q ss_pred HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
.++..||..|++.|+..|.++|+.+|.+|. +++.+++|++||+|+++|+++++|++..+++|.||+++++++.+.++
T Consensus 44 ~~~~~gd~~af~~l~~~y~~~l~~~a~~~~---~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~ 120 (234)
T PRK08301 44 NKLPKGDEAVRSLLIERNLRLVVYIARKFE---NTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMY 120 (234)
T ss_pred HHHHccCHHHHHHHHHHhHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHH
Confidence 334578999999999999999999999998 77889999999999999999999999888899999999999999999
Q ss_pred HH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC--ch
Q 010092 346 MT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQ 422 (518)
Q Consensus 346 I~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~--~~ 422 (518)
++ +.+.. ...+++.+... +.
T Consensus 121 lRk~~~~~---------------------------------------------------------~~~~~~~~~~~~~~~ 143 (234)
T PRK08301 121 LRRNNKVK---------------------------------------------------------AEVSFDEPLNIDWDG 143 (234)
T ss_pred HHHHhccc---------------------------------------------------------cccccccccccccCC
Confidence 98 32110 00011111000 00
Q ss_pred h-h-hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 423 E-E-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 423 e-e-l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
. . ..+...+. ...++...........|..+|+.||+++|.||.|+|||...+++|++|||+.||+|.++|++++++|
T Consensus 144 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA 222 (234)
T PRK08301 144 NELLLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CcccHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0 0 00111111 1112223334445667999999999999999999997766689999999999999999999999999
Q ss_pred HHHHhCcc
Q 010092 501 LMKLKHPT 508 (518)
Q Consensus 501 LkKLR~~~ 508 (518)
+++||+..
T Consensus 223 ~~~Lr~~l 230 (234)
T PRK08301 223 IKRLKKEI 230 (234)
T ss_pred HHHHHHHH
Confidence 99999753
No 35
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=99.91 E-value=5e-23 Score=202.57 Aligned_cols=183 Identities=33% Similarity=0.429 Sum_probs=138.1
Q ss_pred HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (518)
Q Consensus 267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI 346 (518)
++..|+..|++.|+..|.++|+++|.+|. ++..+++||+||+|+++|+++++|+++.+..|.||+++++++.+.+++
T Consensus 41 ~~~~gd~~af~~l~~~y~~~v~~~~~~~~---~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~ 117 (227)
T TIGR02846 41 RLKEGDEEARNVLIERNLRLVAHIVKKFS---NTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHL 117 (227)
T ss_pred HHHcCCHHHHHHHHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHH
Confidence 34578899999999999999999999998 678899999999999999999999999888899999999999999988
Q ss_pred Hh-cCCc-cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092 347 TV-SSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 424 (518)
Q Consensus 347 ~~-sr~i-RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee 424 (518)
++ .+.. +.+. ....+.+... ....
T Consensus 118 Rk~~r~~~~~~~----------------------------------------------------~~~~~~~~~~--~~~~ 143 (227)
T TIGR02846 118 RALKKTKGEVSL----------------------------------------------------QDPIGVDKEG--NEIS 143 (227)
T ss_pred HHHhccccceec----------------------------------------------------cccccCCccc--Cccc
Confidence 83 2110 0000 0000000000 0000
Q ss_pred hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
..+... +....+++.....+....|..+|+.||+++|.||.++|.++..+++|++|||+.||+|.++|++++++|+++|
T Consensus 144 ~~~~~~-~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~L 222 (227)
T TIGR02846 144 LIDILG-SDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222 (227)
T ss_pred HHHHhc-CCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 111111 1122244444555566779999999999999999999965445899999999999999999999999999999
Q ss_pred hCc
Q 010092 505 KHP 507 (518)
Q Consensus 505 R~~ 507 (518)
|+.
T Consensus 223 r~~ 225 (227)
T TIGR02846 223 YKE 225 (227)
T ss_pred HHH
Confidence 964
No 36
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=99.89 E-value=8.8e-22 Score=194.57 Aligned_cols=184 Identities=26% Similarity=0.401 Sum_probs=139.1
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+..+..||..|++.|+..|.+.|+++|.+|. +++.+++||+||+|+++|+++++|++..+++|.||++.++++.+.+
T Consensus 43 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d 119 (234)
T TIGR02835 43 LQKLTQGDESAKSTLIERNLRLVVYIARKFE---NTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILM 119 (234)
T ss_pred HHHHHcCCHHHHHHHHHHhHHHHHHHHHHhc---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHH
Confidence 4445678999999999999999999999998 7888999999999999999999999988888999999999999999
Q ss_pred HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC---C
Q 010092 345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG---V 420 (518)
Q Consensus 345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~---~ 420 (518)
++++ .+.. . ..+++.... .
T Consensus 120 ~~Rk~~r~~-~--------------------------------------------------------~~~~~~~~~~~~~ 142 (234)
T TIGR02835 120 YLRRNNKTR-S--------------------------------------------------------EVSFDEPLNVDWD 142 (234)
T ss_pred HHHHhcccc-C--------------------------------------------------------cccccccccCCCC
Confidence 9983 2110 0 001111000 0
Q ss_pred chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 421 TQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 421 ~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+.........+.+...+++..........|..+|+.||+++|.||.++|.|.+++++|++|||+.||+|..+|++.+++|
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra 222 (234)
T TIGR02835 143 GNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRI 222 (234)
T ss_pred CCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 00000001111111112223334455667999999999999999999997655589999999999999999999999999
Q ss_pred HHHHhCcc
Q 010092 501 LMKLKHPT 508 (518)
Q Consensus 501 LkKLR~~~ 508 (518)
+++||+..
T Consensus 223 ~~~LR~~l 230 (234)
T TIGR02835 223 LKRLKKEI 230 (234)
T ss_pred HHHHHHHh
Confidence 99999754
No 37
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=99.87 E-value=8.3e-21 Score=182.78 Aligned_cols=187 Identities=18% Similarity=0.222 Sum_probs=137.8
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+..+..|+..|++.|+..|.++|+.+|.+|. ++..+++||+||+|++||+++.+|++.+|.+|.||++.++++.+.
T Consensus 14 l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~ 90 (208)
T PRK08295 14 LVELARSGDKEALEYLIEKYKNFVRAKARSYF---LIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQII 90 (208)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence 34556789999999999999999999999998 788999999999999999999999998877999999999999998
Q ss_pred HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
++++. .+..+.+. ....|++.....+.
T Consensus 91 d~~r~~~r~~~~~~----------------------------------------------------~~~~s~~~~~~~~~ 118 (208)
T PRK08295 91 TAIKTANRQKHIPL----------------------------------------------------NSYVSLDKPIYDEE 118 (208)
T ss_pred HHHHHhhhhccccc----------------------------------------------------cceeecCCcccCCc
Confidence 88872 11101110 00112222111000
Q ss_pred --hhhhcccccCCCCcchhhhHHHHHHHHH-HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 423 --EEFINGITDVDGVENENQRQPALLRLAL-DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 423 --eel~~~l~d~~~~~~ee~~~~~~l~~~L-~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..+.+.+.++...+|++.+...+....+ ..+++.||+.++.||.+ | .+++|++|||+.||+|.++|+..+.|
T Consensus 119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~r 193 (208)
T PRK08295 119 SDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQR 193 (208)
T ss_pred cchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHH
Confidence 0111212222223355544444444455 45679999999999999 6 48999999999999999999999999
Q ss_pred HHHHHhCcchh
Q 010092 500 GLMKLKHPTRV 510 (518)
Q Consensus 500 ALkKLR~~~~~ 510 (518)
|+++||.....
T Consensus 194 ar~~Lr~~l~~ 204 (208)
T PRK08295 194 VKRKLEKYLEN 204 (208)
T ss_pred HHHHHHHHHHh
Confidence 99999986543
No 38
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=99.86 E-value=2.9e-20 Score=176.92 Aligned_cols=171 Identities=17% Similarity=0.168 Sum_probs=133.7
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhcc-CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~-~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
+.....|+..|++.|+..|.+.|+.+|.++..+. +...+++|++||+|++||+++.+|++. +..|.+|++..+++.+.
T Consensus 15 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~ 93 (189)
T PRK09648 15 VAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVA 93 (189)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHH
Confidence 5567789999999999999999999999987311 124689999999999999999999864 45799999999999999
Q ss_pred HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
++++ +.+....+ .+
T Consensus 94 d~~r~~~r~~~~~----------------------------------------------------------~~------- 108 (189)
T PRK09648 94 DAHRAAGRDKAVP----------------------------------------------------------TE------- 108 (189)
T ss_pred HHHHHhCCCcccc----------------------------------------------------------cc-------
Confidence 8887 32110000 00
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.+.+.. + ...++++.....+....|..+|..||+++|.||.++| .+++|++|||+.||+|..+|++.++||++
T Consensus 109 -~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 109 -EVPERP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred -cccccc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000000 0 1123455555666777899999999999999999999 58999999999999999999999999999
Q ss_pred HHhCcc
Q 010092 503 KLKHPT 508 (518)
Q Consensus 503 KLR~~~ 508 (518)
+||+..
T Consensus 182 ~Lr~~l 187 (189)
T PRK09648 182 RLRAEI 187 (189)
T ss_pred HHHHHh
Confidence 999753
No 39
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=99.85 E-value=3e-20 Score=177.39 Aligned_cols=185 Identities=18% Similarity=0.237 Sum_probs=136.3
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+..+..||..|++.|+..|.+.|+.+|.++. ++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+
T Consensus 8 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~ 84 (198)
T TIGR02859 8 EIVELARQGNTHALEYLINKYKNFVRAKARSYF---LIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQI 84 (198)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---cccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHH
Confidence 345556789999999999999999999999998 67889999999999999999999999887799999999999988
Q ss_pred HHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC-
Q 010092 343 IRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV- 420 (518)
Q Consensus 343 ~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~- 420 (518)
.++++. .+..+.+. ....|++.+...
T Consensus 85 ~~~~r~~~~~~~~~~----------------------------------------------------~~~~~~~~~~~~~ 112 (198)
T TIGR02859 85 ITAIKTATRQKHIPL----------------------------------------------------NSYVSLNKPIYDE 112 (198)
T ss_pred HHHHHHHHHhcccch----------------------------------------------------hhhcCcccccccc
Confidence 877762 11000000 011222222111
Q ss_pred -chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 421 -TQEEFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 421 -~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.++++.+.+.+....++++.....+....|.++|+. |++.++.|+.. | .+++|++|||+.||+|.++|+..++
T Consensus 113 ~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~-~----~~~~s~~eIA~~l~~s~~tV~~~l~ 187 (198)
T TIGR02859 113 ESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQS-Y----LDGKSYQEIACDLNRHVKSIDNALQ 187 (198)
T ss_pred cccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH-H----HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 111122222222223456666666777789999999 46667777654 5 4899999999999999999999999
Q ss_pred HHHHHHhCc
Q 010092 499 KGLMKLKHP 507 (518)
Q Consensus 499 rALkKLR~~ 507 (518)
+|+++||..
T Consensus 188 r~r~~L~~~ 196 (198)
T TIGR02859 188 RVKRKLEKY 196 (198)
T ss_pred HHHHHHHHh
Confidence 999999974
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=99.85 E-value=1.6e-20 Score=179.36 Aligned_cols=177 Identities=20% Similarity=0.189 Sum_probs=140.1
Q ss_pred HHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHH
Q 010092 262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHA 341 (518)
Q Consensus 262 ~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqa 341 (518)
...+..+..||..|++.|+..|.+.|+++|.++. ++..+++|++||+|+++|++.++|++.. .|.+|++..+++.
T Consensus 14 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~ 88 (194)
T PRK12513 14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL 88 (194)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence 3456677889999999999999999999999998 7788999999999999999999999743 6999999999999
Q ss_pred HHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC
Q 010092 342 IIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV 420 (518)
Q Consensus 342 I~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~ 420 (518)
+.++++ ..+....+. +.
T Consensus 89 ~~~~~R~~~~~~~~~~----------------------------------------------------------~~---- 106 (194)
T PRK12513 89 LIDHWRRHGARQAPSL----------------------------------------------------------DA---- 106 (194)
T ss_pred HHHHHHHhcccccccc----------------------------------------------------------cc----
Confidence 998887 322111000 00
Q ss_pred chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 421 TQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 421 ~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+... .... ....+++...+..+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++.+.||
T Consensus 107 -~~~~-~~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra 179 (194)
T PRK12513 107 -DEQL-HALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYA 179 (194)
T ss_pred -chhh-hhcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 0000 0001 11223455555666778899999999999999999998 589999999999999999999999999
Q ss_pred HHHHhCcchhhh
Q 010092 501 LMKLKHPTRVDY 512 (518)
Q Consensus 501 LkKLR~~~~~~~ 512 (518)
+++||.......
T Consensus 180 ~~~Lr~~l~~~~ 191 (194)
T PRK12513 180 LQKLRELLAEEV 191 (194)
T ss_pred HHHHHHHHHHhh
Confidence 999998766544
No 41
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=99.85 E-value=2.1e-20 Score=174.80 Aligned_cols=174 Identities=16% Similarity=0.118 Sum_probs=134.7
Q ss_pred HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (518)
Q Consensus 267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI 346 (518)
++.+||..|++.|+..|.++|+.++++|. +++.+.+|++||++++||++++.|+ .+.+|.+|++..+++.+.+.+
T Consensus 3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~ 77 (182)
T PRK09652 3 RVQRGDRAAFALLVRRYQPRVKRLLSRLT---RDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYL 77 (182)
T ss_pred hhhcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999999998 6788999999999999999999999 445899999999999999888
Q ss_pred Hh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092 347 TV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 425 (518)
Q Consensus 347 ~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel 425 (518)
+. .+....+ . .+.+.. +....
T Consensus 78 r~~~~~~~~~----~---------------------------------------------------~~~~~~---~~~~~ 99 (182)
T PRK09652 78 RKQGRRPPAS----D---------------------------------------------------VDAEEA---EDFDL 99 (182)
T ss_pred HcccCCCCcc----c---------------------------------------------------cccccc---ccccc
Confidence 73 2210000 0 000000 00000
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+.. + ...++++.+...+....+..+|..|||+++.||.++| ..++|++|||+.||+|..+|++.+++|+++||
T Consensus 100 ~~~~-~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 100 ADAL-R-DISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred cccc-c-cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 0111 1 1123555555666778899999999999999999998 47999999999999999999999999999999
Q ss_pred Ccch
Q 010092 506 HPTR 509 (518)
Q Consensus 506 ~~~~ 509 (518)
+.+.
T Consensus 174 ~~l~ 177 (182)
T PRK09652 174 AKLQ 177 (182)
T ss_pred HHHH
Confidence 7553
No 42
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=99.85 E-value=3e-20 Score=176.41 Aligned_cols=169 Identities=12% Similarity=0.131 Sum_probs=135.1
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+..+..|+..|++.|+..|.++|+.+|.+|. +++.+++|++||+|+++|+++.+|+++ +..|.+|++..+++.+.
T Consensus 10 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~ 85 (186)
T PRK05602 10 LLARVAAGDPAAFRVLVARKLPRLLALATRML---GDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCY 85 (186)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHH
Confidence 45567889999999999999999999999998 788899999999999999999999986 45799999999999888
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++..+.. + .+. ..
T Consensus 86 d~~R~~~~~--~----------------------------------------------------------~~~-----~~ 100 (186)
T PRK05602 86 DRLRRRREV--P----------------------------------------------------------VED-----AP 100 (186)
T ss_pred HHHHhcCCC--C----------------------------------------------------------ccc-----cc
Confidence 877621100 0 000 00
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+ ..+ ....++..+...+....+..+|..||++++.||.++| .+++|++|||+.||+|..+|++.++||+++
T Consensus 101 ~----~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 101 D----VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRA 171 (186)
T ss_pred c----cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 0 000 1112344444455667899999999999999999998 589999999999999999999999999999
Q ss_pred HhCcchh
Q 010092 504 LKHPTRV 510 (518)
Q Consensus 504 LR~~~~~ 510 (518)
||+....
T Consensus 172 Lr~~l~~ 178 (186)
T PRK05602 172 LRAQLAD 178 (186)
T ss_pred HHHHHHh
Confidence 9986654
No 43
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=99.85 E-value=4.6e-20 Score=176.74 Aligned_cols=170 Identities=15% Similarity=0.180 Sum_probs=133.2
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.....|+..|++.|+..|.++|+.+|.+|. ++..+++|++||+|+++|+++++||+..| .|.+|++..+++.+.+
T Consensus 21 i~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~---~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d 96 (194)
T PRK09646 21 LRRVARGDQDAFAELYDRTSSRVYGLVRRVL---RDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVD 96 (194)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHH
Confidence 4556778999999999999999999999999 78899999999999999999999998766 6999999999999988
Q ss_pred HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+++ +.+..+.-. +.. ..
T Consensus 97 ~~r~~~~~~~~~~--------------------------------------------------------~~~------~~ 114 (194)
T PRK09646 97 RVRSEQAASQREV--------------------------------------------------------RYG------AR 114 (194)
T ss_pred HHHhhcccccccc--------------------------------------------------------ccc------cc
Confidence 887 221000000 000 00
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+ .+.....+++.....+....|..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++
T Consensus 115 ---~--~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 115 ---N--VDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIR 185 (194)
T ss_pred ---c--ccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHH
Confidence 0 0000011223333345567899999999999999999998 589999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
||....
T Consensus 186 Lr~~l~ 191 (194)
T PRK09646 186 LRDCLG 191 (194)
T ss_pred HHHHhc
Confidence 997653
No 44
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=99.85 E-value=6.6e-20 Score=170.50 Aligned_cols=167 Identities=18% Similarity=0.196 Sum_probs=133.5
Q ss_pred HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
.+..+||..|++.|+..|.+.+++++.++. ++..+++|++||+|+.+|++.++|+...+ .|.+|++..+++.+.++
T Consensus 3 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~ 78 (170)
T TIGR02952 3 ERAQDREEDAFARIYETYSDRVYRYIYYRV---GCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDY 78 (170)
T ss_pred HHHHccCHHHHHHHHHHHHHHHHHHHHHHH---CChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHH
Confidence 456789999999999999999999999887 67789999999999999999999997555 79999999999999999
Q ss_pred HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092 346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 425 (518)
Q Consensus 346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel 425 (518)
+++.... +. .+++ ..
T Consensus 79 ~R~~~~~--~~-------------------------------------------------------~~~~--------~~ 93 (170)
T TIGR02952 79 FRGSKRH--PL-------------------------------------------------------FSLD--------VF 93 (170)
T ss_pred HHhcCCC--CC-------------------------------------------------------CcHH--------HH
Confidence 8832110 00 0000 00
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+... ...++++.....+....+..+|..|||+++.||.++| .+++|++|||+.||+|..+|++.++||+++||
T Consensus 94 ~~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 94 KELLS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred hhcCC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 00000 1112445555556677899999999999999999998 58999999999999999999999999999999
Q ss_pred Cc
Q 010092 506 HP 507 (518)
Q Consensus 506 ~~ 507 (518)
+.
T Consensus 168 ~~ 169 (170)
T TIGR02952 168 RQ 169 (170)
T ss_pred Hh
Confidence 64
No 45
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=99.84 E-value=5.5e-20 Score=173.80 Aligned_cols=177 Identities=18% Similarity=0.202 Sum_probs=135.8
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+....+|+..|+..|+..|.++|+.+|.+|. +++.+++|++||+|+++|+++..|++.. .|.+|++..+++.+
T Consensus 7 ~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~ 81 (187)
T TIGR02948 7 KRIKEVRKGDENAFADLVDLYKDKIYQLCYRML---GNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLT 81 (187)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHH
Confidence 346667889999999999999999999999998 7788999999999999999999999865 69999999999999
Q ss_pred HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC-Cc
Q 010092 343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG-VT 421 (518)
Q Consensus 343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~-~~ 421 (518)
.++++..+. .. .++.... .+
T Consensus 82 ~~~~rk~~~-~~----------------------------------------------------------~~~~~~~~~~ 102 (187)
T TIGR02948 82 IDRLRKRKP-DF----------------------------------------------------------YLDDEVQGTD 102 (187)
T ss_pred HHHHHhhcc-cc----------------------------------------------------------cccccccCcc
Confidence 888772110 00 0000000 00
Q ss_pred hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.....+...+ ....+++.....+....+..+|+.|||+++.||.++| .+++|++|||+.||+|.++|++.++||+
T Consensus 103 ~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T TIGR02948 103 GLTMESQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred cccccccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 0000011111 1123445555556667799999999999999999988 4899999999999999999999999999
Q ss_pred HHHhCcc
Q 010092 502 MKLKHPT 508 (518)
Q Consensus 502 kKLR~~~ 508 (518)
++||...
T Consensus 178 ~~Lr~~l 184 (187)
T TIGR02948 178 EALRKQL 184 (187)
T ss_pred HHHHHHh
Confidence 9999754
No 46
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=99.84 E-value=6.5e-20 Score=168.25 Aligned_cols=152 Identities=22% Similarity=0.274 Sum_probs=121.5
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCC
Q 010092 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF 351 (518)
Q Consensus 272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~ 351 (518)
+..|++.|+..|.++|+.+++++. ...+++|++||+++++|++++.|++..| .|.+|++..+++.+.+++++..
T Consensus 2 ~~~af~~l~~~y~~~l~~~~~~~~----~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~- 75 (154)
T PRK06759 2 KPATFTEAVVLYEGLIVNQIKKLG----IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEF- 75 (154)
T ss_pred CcccHHHHHHHHHHHHHHHHHHhC----CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHH-
Confidence 457899999999999999998864 4568999999999999999999998776 6999999999999998887210
Q ss_pred ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092 352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431 (518)
Q Consensus 352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d 431 (518)
. .. . . .+ .+
T Consensus 76 -----------------~---~~-----~-----------------------------~-~~----------------~~ 84 (154)
T PRK06759 76 -----------------A---VQ-----E-----------------------------K-CV----------------CV 84 (154)
T ss_pred -----------------h---hc-----c-----------------------------c-cc----------------cc
Confidence 0 00 0 0 00 00
Q ss_pred CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
..+++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++++.||+++||+.
T Consensus 85 ---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 85 ---GEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred ---CCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 00111222234456799999999999999999999 5899999999999999999999999999999963
No 47
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=99.84 E-value=1.6e-19 Score=170.74 Aligned_cols=176 Identities=16% Similarity=0.170 Sum_probs=135.9
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.....|+..|++.|+..|.++|+.+|.++. ++..+++|++||++++||++..+|++.. .|.+|++..+++.+.
T Consensus 8 li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~ 82 (187)
T PRK09641 8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRML---GNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI 82 (187)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence 35566789999999999999999999999998 7888999999999999999999999853 699999999999999
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC-ch
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV-TQ 422 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~-~~ 422 (518)
+++++.+.. . +++..... +.
T Consensus 83 d~~R~~~~~---~--------------------------------------------------------~~~~~~~~~~~ 103 (187)
T PRK09641 83 DRLRKRKPD---Y--------------------------------------------------------YLDAEVAGTEG 103 (187)
T ss_pred HHHHhcCcc---c--------------------------------------------------------cccccccCCcc
Confidence 888732100 0 00000000 00
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
....+.+.+ ...++++.....+....|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++.++||++
T Consensus 104 ~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 104 LTMYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hhhhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 001111111 1223455555566677899999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcc
Q 010092 503 KLKHPT 508 (518)
Q Consensus 503 KLR~~~ 508 (518)
+||...
T Consensus 179 ~Lr~~l 184 (187)
T PRK09641 179 ALRKQL 184 (187)
T ss_pred HHHHHH
Confidence 999754
No 48
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=99.84 E-value=1.2e-19 Score=178.89 Aligned_cols=175 Identities=15% Similarity=0.127 Sum_probs=134.5
Q ss_pred HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (518)
Q Consensus 268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~ 347 (518)
...||..|++.|+..|.++|+.+|.++. ++..+++||+||+|++||++++.|++. ..|.+|++..+++.+.++++
T Consensus 24 ~~~gd~~a~~~l~~~y~~~l~~~a~~~~---~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R 98 (231)
T PRK11922 24 VLAGDEAAFEALMRRHNRRLYRTARAIL---RNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLR 98 (231)
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999999999998 678899999999999999999999986 36999999999999988887
Q ss_pred -hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhh
Q 010092 348 -VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 426 (518)
Q Consensus 348 -~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~ 426 (518)
..+...++. . ..+. ...++..
T Consensus 99 k~~r~~~~~~---------------------------------~----------------------~~~~---~~~~~~~ 120 (231)
T PRK11922 99 RRRRLVNLAE---------------------------------M----------------------VMAS---TIAGGER 120 (231)
T ss_pred hhcccccchh---------------------------------c----------------------cccc---ccccccc
Confidence 221100000 0 0000 0000000
Q ss_pred cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
........++++.....+..+.|..+|+.||+++++||.++| .+++|++|||+.||+|.++|++.+.+|+++||+
T Consensus 121 -~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~ 195 (231)
T PRK11922 121 -TPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLLRE 195 (231)
T ss_pred -cccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 000111223555566667778899999999999999999988 589999999999999999999999999999998
Q ss_pred cchh
Q 010092 507 PTRV 510 (518)
Q Consensus 507 ~~~~ 510 (518)
....
T Consensus 196 ~l~~ 199 (231)
T PRK11922 196 SLAR 199 (231)
T ss_pred HHHH
Confidence 6653
No 49
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=99.83 E-value=1.7e-19 Score=172.20 Aligned_cols=175 Identities=13% Similarity=0.118 Sum_probs=135.9
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+.+...|+..|++.|+..|.++|+.++.++..+.....+++|++||++++||+++++|+++.+ .|.+|++..+++.+
T Consensus 7 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~ 85 (189)
T PRK06811 7 NFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKA 85 (189)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHH
Confidence 34566778999999999999999999999999832112357999999999999999999997655 79999999999999
Q ss_pred HHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc
Q 010092 343 IRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 421 (518)
Q Consensus 343 ~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~ 421 (518)
.++++ +.+.... .+.+.
T Consensus 86 ~d~~rk~~~~~~~---------------------------------------------------------~~~~~----- 103 (189)
T PRK06811 86 IDYKRKLTKNNEI---------------------------------------------------------DSIDE----- 103 (189)
T ss_pred HHHHHHhcccccc---------------------------------------------------------ccchh-----
Confidence 99887 3211000 00000
Q ss_pred hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.. .+ ...++++.....+....|..+|..|||+++.||.++| .+++|++|||+.||+|..+|++.+.||+
T Consensus 104 --~~----~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~ 172 (189)
T PRK06811 104 --FI----LI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGR 172 (189)
T ss_pred --hh----hc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 00 00 0122444455556667799999999999999999988 4899999999999999999999999999
Q ss_pred HHHhCcchhh
Q 010092 502 MKLKHPTRVD 511 (518)
Q Consensus 502 kKLR~~~~~~ 511 (518)
++||....+-
T Consensus 173 ~~Lr~~~~~~ 182 (189)
T PRK06811 173 KKLQKNKLNI 182 (189)
T ss_pred HHHHHcccCc
Confidence 9999865543
No 50
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=99.83 E-value=2.3e-19 Score=169.99 Aligned_cols=171 Identities=19% Similarity=0.199 Sum_probs=129.8
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.....||..|++.|+..|.+.|+.++++|. +++.+++|++||+|+.+|+++++|++..+ .|.+|++..+++.+.
T Consensus 13 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~ 88 (186)
T PRK13919 13 LLALVARGEEEALRALFRRYAGAFLALARRMG---LDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAV 88 (186)
T ss_pred HHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHH
Confidence 34556789999999999999999999999998 67889999999999999999999987643 699999999999999
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+++++.... +.. ++. ...
T Consensus 89 d~~rk~~~~--~~~--------------------------------------------------------~~~----~~~ 106 (186)
T PRK13919 89 DHVRRRAAR--PQP--------------------------------------------------------LEP----DER 106 (186)
T ss_pred HHHHhhhcc--ccc--------------------------------------------------------ccc----ccc
Confidence 888731100 000 000 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+. .. .+. .+++...........|..+|+.||++++.||.++| .+++|++|||+.||+|..+|+..++||+++
T Consensus 107 ~~-~~-~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 107 EP-EA-FDL--PGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSR 178 (186)
T ss_pred cc-cc-ccC--CCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 00 00 000 00111112233456789999999999999999998 589999999999999999999999999999
Q ss_pred HhCcc
Q 010092 504 LKHPT 508 (518)
Q Consensus 504 LR~~~ 508 (518)
||...
T Consensus 179 Lr~~l 183 (186)
T PRK13919 179 LKEVL 183 (186)
T ss_pred HHHHh
Confidence 99643
No 51
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=99.83 E-value=2.2e-19 Score=171.44 Aligned_cols=171 Identities=22% Similarity=0.208 Sum_probs=132.0
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.+...||..|++.|+..|.+.|+.++.++. ++..+++|++||+|+++|+. ..|++..+ .|.||++..+++.+.
T Consensus 19 l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~ 93 (194)
T PRK12519 19 LFSALKAGQSAALGVLYDRHAGLVYGLALKIL---GNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI 93 (194)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence 35556789999999999999999999999998 67789999999999999976 67887655 799999999999999
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+++++.+.. .. ... .. ..
T Consensus 94 d~~Rk~~~~--~~-~~~---------------~~--------------------------------------------~~ 111 (194)
T PRK12519 94 DRLRSRRSR--QR-LLE---------------RW--------------------------------------------QQ 111 (194)
T ss_pred HHHHhcccc--cc-hhh---------------hh--------------------------------------------hh
Confidence 988731100 00 000 00 00
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
... .+....++++.+...+....|..+|..||++++.||.++| .+++|++|||+.||+|.++|++++.||+++
T Consensus 112 ~~~---~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 112 ELL---GEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLK 184 (194)
T ss_pred hhc---ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 000 0001112344444455566789999999999999999998 589999999999999999999999999999
Q ss_pred HhCcc
Q 010092 504 LKHPT 508 (518)
Q Consensus 504 LR~~~ 508 (518)
||...
T Consensus 185 Lr~~l 189 (194)
T PRK12519 185 LRELL 189 (194)
T ss_pred HHHHH
Confidence 99754
No 52
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=99.82 E-value=5.3e-19 Score=167.52 Aligned_cols=177 Identities=12% Similarity=0.086 Sum_probs=134.6
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.....||..|+..|+..|.+.|+.+|.++. ++..+++||+||+|++||+++.+|++. ..|.+|++...++.+.
T Consensus 10 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~ 84 (190)
T TIGR02939 10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYV---RDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAK 84 (190)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHH
Confidence 35556789999999999999999999999998 788899999999999999999999975 3699999999988888
Q ss_pred HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
++++ ..+...... .+.+. .
T Consensus 85 ~~~r~~~r~~~~~~-------------------------------------------------------~~~~~-----~ 104 (190)
T TIGR02939 85 NHLVAQGRRPPTSD-------------------------------------------------------VEIED-----A 104 (190)
T ss_pred HHHHHhccCCCccc-------------------------------------------------------ccccc-----h
Confidence 7776 221100000 00000 0
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+............++++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.++||++
T Consensus 105 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 105 EHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred hhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 00000000001123455555566777899999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||+..+
T Consensus 181 ~Lr~~l~ 187 (190)
T TIGR02939 181 AIAIRLR 187 (190)
T ss_pred HHHHHhh
Confidence 9997653
No 53
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.2e-19 Score=167.37 Aligned_cols=168 Identities=14% Similarity=0.153 Sum_probs=131.7
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.....|+..|+..|+..|.+.|+.+|.+|. ++..+++|++||+|+.+|+++++|++..+ .|.+|++..+++.+.+
T Consensus 10 i~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d 85 (179)
T PRK12514 10 IVRVSLGDRDAFSSLYDATSAKLFGICLRVL---KDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAID 85 (179)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---cCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHH
Confidence 5556789999999999999999999999998 78889999999999999999999997543 6999999999999988
Q ss_pred HHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092 345 SMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 424 (518)
Q Consensus 345 aI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee 424 (518)
++++.+....+ . +. ..+
T Consensus 86 ~~R~~~~~~~~--~--------------------------------------------------------~~-----~~~ 102 (179)
T PRK12514 86 RLRARKAVAVD--I--------------------------------------------------------DE-----AHD 102 (179)
T ss_pred HHHhcCCcccc--c--------------------------------------------------------cc-----chh
Confidence 88731100000 0 00 000
Q ss_pred hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
..+ ...++++.+........|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.+.||+++|
T Consensus 103 ----~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 103 ----LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred ----ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 000 0112344443344456788999999999999999999 5899999999999999999999999999999
Q ss_pred hCcc
Q 010092 505 KHPT 508 (518)
Q Consensus 505 R~~~ 508 (518)
|+..
T Consensus 174 r~~l 177 (179)
T PRK12514 174 RECL 177 (179)
T ss_pred HHHh
Confidence 9754
No 54
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=4.7e-19 Score=170.03 Aligned_cols=171 Identities=17% Similarity=0.095 Sum_probs=135.2
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+.+...||..|++.|+..|.+.|+.+|.++. ++..+++|++||+++.+|+....|++.. ..|.+|++..+++.+
T Consensus 15 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~ 90 (196)
T PRK12524 15 ALLVLYANGDPAAARALTLRLAPRALAVATRVL---GDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLC 90 (196)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHH
Confidence 445667789999999999999999999999998 7889999999999999999999998533 469999999999988
Q ss_pred HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
.+.+++.+... ..++..
T Consensus 91 ~d~~Rk~~~~~----------------------------------------------------------~~~~~~----- 107 (196)
T PRK12524 91 TDRLRRRRRAS----------------------------------------------------------VDLDDA----- 107 (196)
T ss_pred HHHHHhhcCCC----------------------------------------------------------CCcccc-----
Confidence 88777211000 000000
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
. + ..+ ....+++.....+....|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|++.++||++
T Consensus 108 ~---~-~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 108 P---E-PAD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKR 178 (196)
T ss_pred c---c-ccc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 0 000 1112344455556677899999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||....
T Consensus 179 ~Lr~~l~ 185 (196)
T PRK12524 179 ALAALLA 185 (196)
T ss_pred HHHHHHH
Confidence 9997654
No 55
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=99.82 E-value=7.3e-19 Score=167.70 Aligned_cols=177 Identities=11% Similarity=0.062 Sum_probs=134.7
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+..+..||..|++.|+..|.+.|+.++.++. ++..+++|++||+|+.+|+++.+|++.. .|.+|++...++.+.
T Consensus 10 ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~ 84 (193)
T PRK11923 10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFV---HDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK 84 (193)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence 35556788999999999999999999999998 6788999999999999999999999864 589999988888888
Q ss_pred HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
++++ +.+..... ..+++......+
T Consensus 85 d~~rk~~~~~~~~-------------------------------------------------------~~~~~~~~~~~~ 109 (193)
T PRK11923 85 NHLVSRGRRPPDS-------------------------------------------------------DVSSEDAEFYDG 109 (193)
T ss_pred HHHHHhcCCCccc-------------------------------------------------------cccccchhhhcc
Confidence 8776 32210000 000000000000
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.. .+. +...|++.....+....+..+|..||++++.||.++| .+++|++|||+.||+|..+|++...||++
T Consensus 110 ~~---~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 110 DH---ALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRARE 180 (193)
T ss_pred cc---ccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 00 000 1123455555667778899999999999999999988 58999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||....
T Consensus 181 ~Lr~~l~ 187 (193)
T PRK11923 181 AIDKALQ 187 (193)
T ss_pred HHHHHHH
Confidence 9997543
No 56
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=99.82 E-value=7.7e-19 Score=163.76 Aligned_cols=170 Identities=15% Similarity=0.041 Sum_probs=136.2
Q ss_pred HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
.....|+..|++.|+..|.+.|+.+|+++. ++..+.+|++||+++.||.+.+.|+ .+..|.+|++..+++.+.++
T Consensus 5 ~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~ 79 (179)
T PRK11924 5 PVDATGDKEAFSELFRPHAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDL 79 (179)
T ss_pred HHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHH
Confidence 345789999999999999999999999998 7888999999999999999999998 34579999999999999888
Q ss_pred HHhc-CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092 346 MTVS-SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 424 (518)
Q Consensus 346 I~~s-r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee 424 (518)
+++. +..... .+. ..
T Consensus 80 ~r~~~~~~~~~----------------------------------------------------------~~~-----~~- 95 (179)
T PRK11924 80 LRRRRREKAVL----------------------------------------------------------SDD-----AL- 95 (179)
T ss_pred HHhcccccccC----------------------------------------------------------ccc-----cc-
Confidence 8731 110000 000 00
Q ss_pred hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
....+....++++.+...+....|..+|..||++++.||.++| .+++|+.|||+.||+|+.+|++.+.+|+++|
T Consensus 96 --~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 96 --EPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred --ccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 0000002234566677777888999999999999999999998 4799999999999999999999999999999
Q ss_pred hCcchh
Q 010092 505 KHPTRV 510 (518)
Q Consensus 505 R~~~~~ 510 (518)
|+....
T Consensus 170 r~~l~~ 175 (179)
T PRK11924 170 RECLEA 175 (179)
T ss_pred HHHHHH
Confidence 976543
No 57
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=99.82 E-value=3.5e-19 Score=169.74 Aligned_cols=160 Identities=18% Similarity=0.223 Sum_probs=125.3
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
||..|++.|+..|.+.|+.+|.+|. ++..+++|++||+|+.+|+++++|++. ..|.+|++.++++.+.++++...
T Consensus 23 gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~ 97 (188)
T PRK09640 23 HVTRAYEELMRRYQRTLFNVCARYL---GNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSITYNECITQYRKER 97 (188)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHHHHHHHHHHHHhc
Confidence 6999999999999999999999999 788899999999999999999999863 37999999999999998887311
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
..... .. + ...+...
T Consensus 98 ~~~~~---~~------------------------------------------------------~--------~~~~~~~ 112 (188)
T PRK09640 98 RKRRL---MD------------------------------------------------------A--------LSLDPLE 112 (188)
T ss_pred ccccC---cc------------------------------------------------------h--------hhhcccc
Confidence 00000 00 0 0000000
Q ss_pred cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
+.. ++.....+....|..+|+.||++++.||.++| .+++|++|||+.||||..+|+..+.||+++||...
T Consensus 113 ~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 113 EAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred ccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 000 01111224456799999999999999999999 58999999999999999999999999999999754
No 58
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=5.6e-19 Score=167.47 Aligned_cols=168 Identities=15% Similarity=0.128 Sum_probs=131.8
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+..+..|+..|++.|+..|.+.++.++.++. ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+.
T Consensus 13 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~ 88 (182)
T PRK12537 13 CLLACARGDRRALQALYQQESARLLGVARRIV---RDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLAL 88 (182)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence 45667789999999999999999999999998 78889999999999999999999986443 699999999999998
Q ss_pred HHHHhcC-CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMTVSS-FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~~sr-~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
++++..+ ... .+.. .
T Consensus 89 d~~r~~~~~~~------------------------------------------------------------~~~~----~ 104 (182)
T PRK12537 89 NVLRDTRREVV------------------------------------------------------------LDDD----A 104 (182)
T ss_pred HHHHhccccCc------------------------------------------------------------cccc----h
Confidence 8887311 000 0000 0
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.+...+ ..++++..........|..+|+.||++++.||.++| .+++|++|||+.||+|..+|+..++||++
T Consensus 105 ---~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 105 ---EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred ---hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 000000 011222233334556789999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcc
Q 010092 503 KLKHPT 508 (518)
Q Consensus 503 KLR~~~ 508 (518)
+||...
T Consensus 176 ~Lr~~l 181 (182)
T PRK12537 176 ALRECM 181 (182)
T ss_pred HHHHHh
Confidence 999753
No 59
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=6e-19 Score=167.47 Aligned_cols=170 Identities=19% Similarity=0.183 Sum_probs=132.3
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.....|+..+++.|+..|.++|+++|.++. ++..+++|++||+|+.+|++.++|++..+ .|.+|++..+++.+.+
T Consensus 16 ~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d 91 (187)
T PRK12534 16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMI---PQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID 91 (187)
T ss_pred HHHHHcCCHHHHHHHHHHhhHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence 4455678999999999999999999999998 77889999999999999999999998654 5889999999999888
Q ss_pred HHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092 345 SMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 424 (518)
Q Consensus 345 aI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee 424 (518)
++++....+.. .+++.
T Consensus 92 ~~R~~~~~~~~--------------------------------------------------------~~~~~-------- 107 (187)
T PRK12534 92 HLRANAPQRRN--------------------------------------------------------VALDD-------- 107 (187)
T ss_pred HHHhccccccc--------------------------------------------------------ccccc--------
Confidence 87731100000 00000
Q ss_pred hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
.... .+ ...++++.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.++||+++|
T Consensus 108 ~~~~-~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 181 (187)
T PRK12534 108 AGEL-RA-ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKL 181 (187)
T ss_pred hhhh-cc-ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 0000 00 0111233334456677899999999999999999999 5899999999999999999999999999999
Q ss_pred hCcc
Q 010092 505 KHPT 508 (518)
Q Consensus 505 R~~~ 508 (518)
|...
T Consensus 182 r~~l 185 (187)
T PRK12534 182 KACL 185 (187)
T ss_pred HHHH
Confidence 9753
No 60
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=8.2e-19 Score=173.75 Aligned_cols=169 Identities=14% Similarity=0.156 Sum_probs=133.6
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+..+..||..|++.|+..|.+.|+.++.++. ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
T Consensus 52 ~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~---~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~ 127 (233)
T PRK12538 52 ELLDRLATDDEAAFRLLVERHIDRAYAIALRIV---GNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC 127 (233)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence 345567789999999999999999999999998 77789999999999999999999987544 69999999999888
Q ss_pred HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
.+++++.+.. . ++. .
T Consensus 128 id~~Rk~~~~-------~-----------------------------------------------------~~~-----~ 142 (233)
T PRK12538 128 IDLRRKPRTE-------N-----------------------------------------------------VDA-----V 142 (233)
T ss_pred HHHHHhhccc-------c-----------------------------------------------------ccc-----c
Confidence 8777621100 0 000 0
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
. +. .+ ...++++.....+....|..+|..||+++|.||.|+| .+++|++|||+.||+|.++|++.++||++
T Consensus 143 ~---~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~ 213 (233)
T PRK12538 143 P---EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQ 213 (233)
T ss_pred c---cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 0 00 00 0112233344456667899999999999999999999 68999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||+...
T Consensus 214 kLr~~l~ 220 (233)
T PRK12538 214 QLRDLLR 220 (233)
T ss_pred HHHHHHH
Confidence 9998654
No 61
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.4e-19 Score=167.70 Aligned_cols=175 Identities=14% Similarity=0.130 Sum_probs=132.6
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.+...||..|++.|+..|.+.|+.+|.++. ++..+++|++||+|+.+|+...+|++..+ .|.+|++..+++.+.+
T Consensus 18 i~~~~~~d~~af~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld 93 (194)
T PRK12531 18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHV---GNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD 93 (194)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence 6667889999999999999999999999998 67788999999999999999999997554 6999999999999998
Q ss_pred HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++ .+... .. .. +... ..+
T Consensus 94 ~~Rk~~~~~~-~~--~~------------------------------------------------------~~~~--~~~ 114 (194)
T PRK12531 94 LLRKQKGKDL-HI--HA------------------------------------------------------DDIW--PSD 114 (194)
T ss_pred HHHHhccccc-cc--ch------------------------------------------------------hhcc--ccc
Confidence 8873 21000 00 00 0000 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
....... ....++ .......+..+|..||++++.||.++| .+++|++|||+.||+|..+|+..+++|+++
T Consensus 115 ~~~~~~~--~~~~~e----~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 115 YYPPDLV--DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEK 184 (194)
T ss_pred ccccccc--cccCHH----HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 0000000 001111 123346788999999999999999998 589999999999999999999999999999
Q ss_pred HhCcchhhh
Q 010092 504 LKHPTRVDY 512 (518)
Q Consensus 504 LR~~~~~~~ 512 (518)
||.....+.
T Consensus 185 Lr~~l~~~~ 193 (194)
T PRK12531 185 LRHSMDAES 193 (194)
T ss_pred HHHHhhhcc
Confidence 998766544
No 62
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=99.81 E-value=9.8e-19 Score=166.60 Aligned_cols=173 Identities=16% Similarity=0.140 Sum_probs=136.5
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+.....||..|++.|+..|.+.++.++.++. ++..+.+|++||+|+.+|++.+.|++. ..|.+|++..+++.+
T Consensus 11 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~ 85 (189)
T PRK12515 11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLV---RDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKA 85 (189)
T ss_pred HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHH
Confidence 445667889999999999999999999999998 778899999999999999999999964 379999999999998
Q ss_pred HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
.+++++.+.. +. ..
T Consensus 86 ~d~~r~~~~~--~~----------------------------------------------------------~~------ 99 (189)
T PRK12515 86 LSALRRRKHE--EI----------------------------------------------------------DD------ 99 (189)
T ss_pred HHHHHccCCC--CC----------------------------------------------------------cc------
Confidence 8887721100 00 00
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+......+ ...++++.....++...+..+|+.||++++.||.++| .+++|++|||+.||+|..+|++.+.||++
T Consensus 100 -~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 100 -EAAAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred -ccccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 00000011 1122444444556667899999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcchhhh
Q 010092 503 KLKHPTRVDY 512 (518)
Q Consensus 503 KLR~~~~~~~ 512 (518)
+||+......
T Consensus 174 ~Lr~~l~~~~ 183 (189)
T PRK12515 174 KLAELLKAAG 183 (189)
T ss_pred HHHHHHHHhc
Confidence 9998765543
No 63
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=99.80 E-value=1.6e-18 Score=155.47 Aligned_cols=155 Identities=23% Similarity=0.286 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (518)
Q Consensus 275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR 353 (518)
|++.|+..|.++|.++++++. .++.+.+|++|||+++||++++.|++. ..|.+|+.+++++.+.++++ +.+
T Consensus 2 a~~~l~~~~~~~v~~~~~~~~---~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~--- 73 (158)
T TIGR02937 2 AFEELYERYLPLLYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR--- 73 (158)
T ss_pred HHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---
Confidence 789999999999999999998 677889999999999999999999998 58999999999999999988 322
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~ 433 (518)
.+..+.. .. .. ...
T Consensus 74 ~~~~~~~-------------------------------------------------------------~~----~~-~~~ 87 (158)
T TIGR02937 74 LRRELDL-------------------------------------------------------------LE----EL-LDS 87 (158)
T ss_pred CCcchhh-------------------------------------------------------------hh----hc-ccc
Confidence 1100000 00 00 001
Q ss_pred CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
...+++..........|..+|+.||+.++.||.++| ..++|..|||+.||+|+.+|+++..+++++||+.
T Consensus 88 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 88 DPSPEEELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 112444455566777899999999999999999998 4789999999999999999999999999999963
No 64
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=4.1e-19 Score=168.62 Aligned_cols=171 Identities=17% Similarity=0.149 Sum_probs=130.3
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
..||..|+..|+..|.+.++.+|.++. ++..+++|++||.|+.+|++.++|++..+..|.||++..+++.+.+++++
T Consensus 4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk 80 (185)
T PRK12542 4 TNNDYEKMEELYELYEQKVYYVAYSIL---NNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK 80 (185)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999 67788999999999999999999987544579999999999999888872
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~ 428 (518)
... ...+... .+ .. .
T Consensus 81 ~~~----------------------~~~~~~~---------------------------------~~-------~~---~ 95 (185)
T PRK12542 81 NKR----------------------HETFLEE---------------------------------YE-------RE---S 95 (185)
T ss_pred hhh----------------------hhhhhhh---------------------------------cc-------cc---c
Confidence 110 0000000 00 00 0
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
.... ...+++.....+....|..+|..|||++++||.|+| .+++|++|||+.||+|..+|+..+.||+++||...
T Consensus 96 ~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 96 IEAV-DENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hhhh-hccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 0000 011222222333446789999999999999999998 58999999999999999999999999999999866
Q ss_pred hhhh
Q 010092 509 RVDY 512 (518)
Q Consensus 509 ~~~~ 512 (518)
....
T Consensus 171 ~~~~ 174 (185)
T PRK12542 171 GGIQ 174 (185)
T ss_pred cccc
Confidence 5443
No 65
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=99.80 E-value=1.5e-18 Score=164.04 Aligned_cols=182 Identities=15% Similarity=0.138 Sum_probs=133.8
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhc-cCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQD-FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~-~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
.|+..|++.|+..|.+.|+.+|++|... +++..+++|++||+++.+|+++..|+...+..|.+|++..+++.+.+++++
T Consensus 3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~ 82 (189)
T TIGR02984 3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR 82 (189)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999997531 235678999999999999999999997666689999999999999888762
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC--chhhhh
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQEEFI 426 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~--~~eel~ 426 (518)
.. ... .+. + ....+++..... ....+.
T Consensus 83 ~~----------------~~~----~r~--------~-----------------------~~~~~~~~~~~~~~~~~~~~ 111 (189)
T TIGR02984 83 HL----------------GAQ----KRD--------I-----------------------RREQSLDAGGRLDESSVRLA 111 (189)
T ss_pred HH----------------HHH----hhh--------c-----------------------ccccCCCcccccCCcchhHH
Confidence 10 000 000 0 000112211100 011122
Q ss_pred cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.+.+ ...++++.....+....|..+|..|||+++.||.++| ..++|++|||+.||||.++|++.++||+++||+
T Consensus 112 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 112 AQLAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred HHccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 22222 2223555555566667899999999999999999999 489999999999999999999999999999996
Q ss_pred c
Q 010092 507 P 507 (518)
Q Consensus 507 ~ 507 (518)
.
T Consensus 187 ~ 187 (189)
T TIGR02984 187 I 187 (189)
T ss_pred H
Confidence 4
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=99.80 E-value=1.9e-18 Score=167.42 Aligned_cols=173 Identities=12% Similarity=0.153 Sum_probs=131.4
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.....|+..|++.|+..|.+.|+.++.++. ++..+++|++||+|+.+|+++..|++.++ .|.+|++.++++.+.+
T Consensus 29 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d 104 (206)
T PRK12526 29 ILVAISRDKQAFTHLFQFFAPKIKRFGIKQL---GNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD 104 (206)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence 3345679999999999999999999999998 67788999999999999999999997665 5999999999999999
Q ss_pred HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+++ +.+..... ..++ ..+
T Consensus 105 ~~Rk~~~~~~~~------------------------------~~~~---------------------~~~---------- 123 (206)
T PRK12526 105 MLRKIKAKKEQN------------------------------LGDD---------------------IWP---------- 123 (206)
T ss_pred HHHHhccccccc------------------------------cccc---------------------cch----------
Confidence 887 32110000 0000 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
..+.+.+.. . .............|..+|..||++++.||.++| .+++|++|||+.||+|..+|+..+++|+++
T Consensus 124 -~~~~~~~~~-~-~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 124 -IEQALAESQ-S-ESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAK 196 (206)
T ss_pred -hhhhccccc-C-chHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 000001110 1 111222333456799999999999999999999 589999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
||....
T Consensus 197 Lr~~l~ 202 (206)
T PRK12526 197 LKVQMG 202 (206)
T ss_pred HHHHHh
Confidence 997654
No 67
>TIGR02895 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).
Probab=99.80 E-value=3.6e-18 Score=167.48 Aligned_cols=186 Identities=13% Similarity=0.175 Sum_probs=134.4
Q ss_pred HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM 346 (518)
Q Consensus 267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI 346 (518)
.+.+||.. ++.||..|.|+|.++|.+|..+. .+.+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++
T Consensus 3 ~~~~gd~~-~e~LI~~Y~plI~~~a~~~~~~~-~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dyl 80 (218)
T TIGR02895 3 PIQPGNEE-REELIRQYKPFIAKIVSSVCGRY-IDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYI 80 (218)
T ss_pred hhhcCChH-HHHHHHHhHHHHHHHHHHHHccC-CCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 35678877 99999999999999999997321 13589999999999999999999999999999999999999999999
Q ss_pred H-hc---CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh------CCCHHHHHHHHHhcCCccccCC
Q 010092 347 T-VS---SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGV------NISPERYREVMKASKPILSLHS 416 (518)
Q Consensus 347 ~-~s---r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~l------gis~e~v~~~l~~~~~~~SLD~ 416 (518)
+ .. ..+++|....+ ....+..+..++..++++.|+.+||+..- |+|.+++-+
T Consensus 81 Rk~~k~~~~v~~~~~~~e-----~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~------------- 142 (218)
T TIGR02895 81 RKNQKYQNLLYLDEDYDE-----NPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK------------- 142 (218)
T ss_pred HhcccccCeeeCCchHHH-----HHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh-------------
Confidence 9 44 46688865554 56677777888999999999999998542 444443211
Q ss_pred CcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010092 417 RHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 496 (518)
Q Consensus 417 ~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqi 496 (518)
. +|-+ -+.....-.+...+. ....++..-+. ...+.++||+..++||+.++.+.
T Consensus 143 ---------------~---sPkh-~d~r~~~i~ia~~~~----~~~~l~~~l~~---kk~LP~k~l~~~~~v~rktier~ 196 (218)
T TIGR02895 143 ---------------V---SPKH-RDTRKKAIKIAKVIV----ENEELLEYLIR---KKKLPIKEIEERVRISRKTIERY 196 (218)
T ss_pred ---------------c---CCCC-HHHHHHHHHHHHHHh----cCHHHHHHHHH---hCCCCHHHHHHHcCCCHHHHHHh
Confidence 0 1111 111122222322222 12222322221 35789999999999999999875
Q ss_pred HH
Q 010092 497 EV 498 (518)
Q Consensus 497 e~ 498 (518)
..
T Consensus 197 rk 198 (218)
T TIGR02895 197 RK 198 (218)
T ss_pred hH
Confidence 44
No 68
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=99.79 E-value=4.6e-18 Score=155.60 Aligned_cols=160 Identities=16% Similarity=0.184 Sum_probs=124.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR 353 (518)
.|++.|+..|.+.|+.+++++. ++..+.+|++||+++++|+++.+|++.. +|.+|++.++++.+.++++...
T Consensus 1 ~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~--- 72 (161)
T TIGR02985 1 KAFEQLYRRYYPKLCAFAYRYV---KDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQ--- 72 (161)
T ss_pred ChHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHH---
Confidence 3789999999999999999998 6788899999999999999999998643 7999999999999998887211
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~ 433 (518)
........+... + .....
T Consensus 73 ---------------~~~~~~~~~~~~----------------------------------~-------------~~~~~ 90 (161)
T TIGR02985 73 ---------------VEEKYQEEILEI----------------------------------E-------------VDELS 90 (161)
T ss_pred ---------------hHhHHHHHHHhh----------------------------------c-------------ccccC
Confidence 000000000000 0 00001
Q ss_pred CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
..++++.+...++...|..+|..||++++.||.++| .+++|..|||+.||+|+++|++.+.+|+++||+.
T Consensus 91 ~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 91 ENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 112444455566777899999999999999999988 4899999999999999999999999999999964
No 69
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=4e-18 Score=161.21 Aligned_cols=165 Identities=16% Similarity=0.093 Sum_probs=128.6
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
.|+..|+..|+..|.+.|+.++..|. ++..+.+|++||+|+.+|+++.+|++.. .|.+|++..+++.+.++++..
T Consensus 3 ~~d~~af~~l~~~~~~~l~~~~~~~~---~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~ 77 (179)
T PRK12543 3 SGDQEAFSEIYDVTIQEVYKTVHFLV---EDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKR 77 (179)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhh
Confidence 57889999999999999999999998 7888999999999999999999999864 699999988888887766521
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 429 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l 429 (518)
..-.. .++.. .+..+.
T Consensus 78 ~~~~~----------------------------------------------------------~~~~~-----~~~~~~- 93 (179)
T PRK12543 78 WRRFR----------------------------------------------------------IFEKA-----EEQRKP- 93 (179)
T ss_pred ccccc----------------------------------------------------------ccccc-----cccccc-
Confidence 10000 00000 000000
Q ss_pred ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.....++. ....+....|..+|..|||++|.||.|+| .+++|++|||+.||+|..+|+..+++|+++||+.+.
T Consensus 94 --~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 94 --VSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred --ccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 00112333 45556677899999999999999999998 589999999999999999999999999999998665
Q ss_pred h
Q 010092 510 V 510 (518)
Q Consensus 510 ~ 510 (518)
.
T Consensus 167 ~ 167 (179)
T PRK12543 167 I 167 (179)
T ss_pred H
Confidence 4
No 70
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=99.79 E-value=6e-18 Score=162.15 Aligned_cols=167 Identities=13% Similarity=0.101 Sum_probs=133.2
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
..+.....|+..+++.|+..|.+.|++++.++. ++..+++|++||+|+.+|++.++|++.. .|.+|++..+++.+
T Consensus 16 ~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~ 90 (192)
T PRK09643 16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNAC 90 (192)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHH
Confidence 345567789999999999999999999999998 7888999999999999999999999753 69999999999999
Q ss_pred HHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc
Q 010092 343 IRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 421 (518)
Q Consensus 343 ~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~ 421 (518)
.+++++ .+.... +++.
T Consensus 91 ~d~~Rk~~~~~~~----------------------------------------------------------~~~~----- 107 (192)
T PRK09643 91 LDRLRRAKARPTV----------------------------------------------------------PLDD----- 107 (192)
T ss_pred HHHHHccccCCCC----------------------------------------------------------Cccc-----
Confidence 998883 211000 0000
Q ss_pred hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.. .... .+++.....+....|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|+..+.+|+
T Consensus 108 ~~----~~~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar 175 (192)
T PRK09643 108 VY----PVAQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGR 175 (192)
T ss_pred cc----cccC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 00 0000 1122233445567799999999999999999998 5899999999999999999999999999
Q ss_pred HHHhCcch
Q 010092 502 MKLKHPTR 509 (518)
Q Consensus 502 kKLR~~~~ 509 (518)
++||....
T Consensus 176 ~~Lr~~l~ 183 (192)
T PRK09643 176 ARLAELLG 183 (192)
T ss_pred HHHHHHHH
Confidence 99997654
No 71
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=99.79 E-value=5e-18 Score=160.79 Aligned_cols=168 Identities=15% Similarity=0.112 Sum_probs=129.2
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.....||..|++.|+..|.+.|+.++.++.. +...+++|++||+|+.||+..+.|++. ..|.+|++..+++.+.
T Consensus 11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~--~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~ 86 (181)
T PRK12536 11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLP--QLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM 86 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC--CChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence 356778899999999999999999999988652 346799999999999999999999974 3699999999999999
Q ss_pred HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
+++++ .+.. +.+ .+++
T Consensus 87 d~~Rk~~~~~--~~~------------------------------------------------------~~~~------- 103 (181)
T PRK12536 87 DFLRSRARRE--ALH------------------------------------------------------DPLD------- 103 (181)
T ss_pred HHHHHHhccc--ccc------------------------------------------------------CCcc-------
Confidence 88873 1110 000 0000
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+..+...+. . ++ ..+....+..+|..||++++.||.++| .+++|++|||+.||+|.++|+..+++|++
T Consensus 104 -~~~~~~~~~-~--~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 104 -DESELFATS-D--DE----AAEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLK 171 (181)
T ss_pred -chhhhcCCC-C--cc----hHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 000000000 0 11 123445689999999999999999998 58999999999999999999999999999
Q ss_pred HHhCcchh
Q 010092 503 KLKHPTRV 510 (518)
Q Consensus 503 KLR~~~~~ 510 (518)
+||+.+..
T Consensus 172 ~Lr~~l~~ 179 (181)
T PRK12536 172 ALAAKIRG 179 (181)
T ss_pred HHHHHhcC
Confidence 99986543
No 72
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=7.6e-18 Score=159.49 Aligned_cols=167 Identities=16% Similarity=0.187 Sum_probs=127.6
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccC-CCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~-~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
+.....||..|++.|+..|.+.|+.+|.++..+.+ +..+++|++||+++.+|...+.|+.. ..|.+|++..+++.+.
T Consensus 13 ~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~ 90 (184)
T PRK12512 13 MRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLI 90 (184)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHH
Confidence 44567799999999999999999999999874211 34689999999999999999999864 3699999999999998
Q ss_pred HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
+++++ .+...+ +++
T Consensus 91 d~~Rr~~~~~~~----------------------------------------------------------~~~------- 105 (184)
T PRK12512 91 DALRRRGRRVFV----------------------------------------------------------DID------- 105 (184)
T ss_pred HHHHhhcccccC----------------------------------------------------------Cch-------
Confidence 88872 111000 000
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
++.+.+.+.. .. .......+..+|+.||+++++||.++| .+++|++|||+.||+|..+|+..+++|++
T Consensus 106 -~~~~~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 106 -DFAETLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred -hccccccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 0000000100 00 112345688899999999999999998 58999999999999999999999999999
Q ss_pred HHhCcchh
Q 010092 503 KLKHPTRV 510 (518)
Q Consensus 503 KLR~~~~~ 510 (518)
+||...++
T Consensus 174 ~Lr~~l~~ 181 (184)
T PRK12512 174 ALAAKFRS 181 (184)
T ss_pred HHHHHhhc
Confidence 99976654
No 73
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=99.78 E-value=3.5e-18 Score=160.39 Aligned_cols=167 Identities=16% Similarity=0.126 Sum_probs=129.1
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+....+||..|++.|+..|.+.|+.+|.+|. ++..+++|++||+|+++|++++.|++. .+|.+|++..+++.+.
T Consensus 8 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~ 82 (176)
T PRK09638 8 LIQKAKKGDDAALTTLFQQHYSFLYKYLLKLT---LDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYK 82 (176)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHH
Confidence 34566789999999999999999999999998 778889999999999999999999864 3799999999999999
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++..+.. .+ .. +. ..+
T Consensus 83 d~~r~~~~~-~~---------------------~~---------~~-----------------------~~~-------- 100 (176)
T PRK09638 83 DHLRKQKRE-KL---------------------RL---------QR-----------------------AKE-------- 100 (176)
T ss_pred HHHHHhccc-cc---------------------hh---------hh-----------------------ccc--------
Confidence 888731100 00 00 00 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
...+.. .. +..........|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.+.||+++
T Consensus 101 ----~~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 101 ----ETLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred ----ccCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 000000 00 1112223445688999999999999999988 579999999999999999999999999999
Q ss_pred HhCcc
Q 010092 504 LKHPT 508 (518)
Q Consensus 504 LR~~~ 508 (518)
||+..
T Consensus 170 l~~~l 174 (176)
T PRK09638 170 LRKEW 174 (176)
T ss_pred HHHHh
Confidence 99743
No 74
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=99.78 E-value=9.4e-18 Score=157.51 Aligned_cols=164 Identities=12% Similarity=0.013 Sum_probs=125.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT 352 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~i 352 (518)
..++.|+..|.++|+.+|.+|. ++..+++|++||+++.||++.+.|++.. +|.+|++..+++.+.++++ +.+..
T Consensus 3 ~~~~~l~~~y~~~i~~~~~~~~---~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~ 77 (173)
T PRK12522 3 EKVEELIDIYKQQIYSLCYKLA---KTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWK 77 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccc
Confidence 4689999999999999999998 7889999999999999999999999754 7999999999999999888 32210
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
..+.... + .+...+.....
T Consensus 78 ~~~~~~~-------------------------------------------------------~------~~~~~~~~~~~ 96 (173)
T PRK12522 78 DRILDLF-------------------------------------------------------H------KEDGGEIEFAD 96 (173)
T ss_pred ccccccc-------------------------------------------------------c------hhhhhhhcccc
Confidence 0000000 0 00000000000
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
....++. ....+..+.|..+|..||++++.||.|+| .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus 97 ~~~~~~~-~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 97 DVNISEE-FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CCCChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 1111222 34455677899999999999999999999 68999999999999999999999999999999654
No 75
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=99.77 E-value=9.1e-18 Score=158.91 Aligned_cols=163 Identities=15% Similarity=0.060 Sum_probs=129.3
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
..+..|++.|+..|.+.|+.+|.++. ++..+++|++||+|+.||++..+|+.. ..|.+|++..+++.+.+++++.
T Consensus 12 ~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~ 86 (179)
T PRK09415 12 EDKEDLIDEIMNEYGQEVLQLVYSYV---KNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSW 86 (179)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999999999998 778899999999999999999999864 3699999999999998888731
Q ss_pred -CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092 350 -SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 350 -r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~ 428 (518)
+....+ .+. ..+.
T Consensus 87 ~~~~~~~----------------------------------------------------------~~~--------~~~~ 100 (179)
T PRK09415 87 HNKKVIV----------------------------------------------------------TED--------IFTY 100 (179)
T ss_pred ccccccc----------------------------------------------------------ccc--------cccc
Confidence 100000 000 0000
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
.. ....++++.....+....|..+|+.||+++++||.++| .+++|++|||+.||+|..+|++.+.||+++||...
T Consensus 101 ~~-~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 101 ME-SQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred cc-ccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 00 01123445555566777899999999999999999998 58999999999999999999999999999999754
No 76
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=99.77 E-value=9.9e-18 Score=156.61 Aligned_cols=162 Identities=25% Similarity=0.226 Sum_probs=127.5
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+..+..||..|++.|+..|.+.+++++.++. ++..+++|++||+++.+|+..+.|++.. .|.+|++..+++.+.
T Consensus 6 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~ 80 (169)
T TIGR02954 6 LVKKAKRGNKPAFESLIKKHKEKLYKTAFIYV---KNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECI 80 (169)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHH
Confidence 35567789999999999999999999999999 7888999999999999999999999753 699999999999999
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++.... ..| ++....
T Consensus 81 d~~R~~~~-~~~----------------------------------------------------------~~~~~~---- 97 (169)
T TIGR02954 81 DLLKKKKK-VIP----------------------------------------------------------FDPNTS---- 97 (169)
T ss_pred HHHHhcCC-cCc----------------------------------------------------------cccccc----
Confidence 88873110 000 000000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
..+. .++. + ......|..+|+.||+++++||.++| .+++|++|||+.||+|..+|+..+.||+++
T Consensus 98 -----~~~~---~~~~--~-~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 98 -----IEKG---ECET--H-ADSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKK 162 (169)
T ss_pred -----cccc---hhhh--c-hHHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0000 0000 0 01123788999999999999999998 589999999999999999999999999999
Q ss_pred HhCcc
Q 010092 504 LKHPT 508 (518)
Q Consensus 504 LR~~~ 508 (518)
||..+
T Consensus 163 Lr~~l 167 (169)
T TIGR02954 163 LKKRL 167 (169)
T ss_pred HHHHh
Confidence 99754
No 77
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=99.77 E-value=1.5e-17 Score=157.91 Aligned_cols=168 Identities=16% Similarity=0.181 Sum_probs=127.7
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhcc-CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~-~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
+.+...||..|++.|+..|.+.|+.+|.+...++ ++..+.+|++||+++.+|++.+.|++.. .|.+|++..+++.+.
T Consensus 12 ~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~ 89 (184)
T PRK12539 12 MLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLI 89 (184)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHH
Confidence 4567789999999999999999999987533211 5778999999999999999999999753 699999999999998
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++.......+ .+++. .
T Consensus 90 d~~R~~~~~~~~--------------------------------------------------------~~~~~-----~- 107 (184)
T PRK12539 90 DHLRRTRASLAD--------------------------------------------------------VPIDD-----A- 107 (184)
T ss_pred HHHHHHhccccc--------------------------------------------------------cChhh-----h-
Confidence 888721100000 00000 0
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+... +.+.....+....|..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.+++|+++
T Consensus 108 ---~~~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~ 174 (184)
T PRK12539 108 ---DELV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLKA 174 (184)
T ss_pred ---cccc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0000 001112223456799999999999999999998 589999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
||+...
T Consensus 175 Lr~~l~ 180 (184)
T PRK12539 175 LAALIG 180 (184)
T ss_pred HHHHHh
Confidence 997543
No 78
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=99.77 E-value=1.2e-17 Score=156.47 Aligned_cols=163 Identities=15% Similarity=0.166 Sum_probs=126.2
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
.++..+++.|+..|.+.|+.+|.++. ++..+++|++||.|+.+|+..++|++.. ..|.+|++..+++.+.+++++.
T Consensus 5 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~ 80 (173)
T PRK09645 5 TAEAALMRALYDEHAAPLWRYALRLT---GDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSA 80 (173)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhh
Confidence 36789999999999999999999998 6778999999999999999999997533 3699999999999999888731
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 429 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l 429 (518)
+.. +.. . .+ +... .
T Consensus 81 ~~~--~~~--~-----------------------------------------------------~~--------~~~~-~ 94 (173)
T PRK09645 81 RAR--PVE--G-----------------------------------------------------GD--------DVLG-V 94 (173)
T ss_pred ccc--ccc--c-----------------------------------------------------cc--------cccc-C
Confidence 100 000 0 00 0000 0
Q ss_pred ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.+ ..+++..........|..+|+.||+++++||.|+| .+++|++|||+.||+|..+|+..++||+++||+.+.
T Consensus 95 ~~---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 95 PE---QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CC---CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 00 01122233334455789999999999999999999 589999999999999999999999999999998654
No 79
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=99.77 E-value=1e-17 Score=159.68 Aligned_cols=168 Identities=16% Similarity=0.118 Sum_probs=128.5
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.++..|+..|++.|+..|.+.++.++. +. ++..+++|++||.|+.+|+..++|++. ..|.+|++..+++.+.+
T Consensus 15 ~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~---~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d 88 (185)
T PRK09649 15 ALSAAKGNGRALEAFIKATQQDVWRFVA-YL---SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD 88 (185)
T ss_pred HHHHHccCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence 5567789999999999999999999995 55 677899999999999999999999864 36999999999999998
Q ss_pred HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
++++ .+..+.. .+. ..+
T Consensus 89 ~~Rk~~~~~~~~----------------------------------------------------------~~~----~~~ 106 (185)
T PRK09649 89 HIRHVRSRPRTT----------------------------------------------------------RGA----RPE 106 (185)
T ss_pred HHHHhccccccc----------------------------------------------------------ccc----chh
Confidence 8872 1100000 000 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
...+ ++......+....|..+|+.||+++|.||.|+| .+++|++|||+.||+|.++|++.+.||+++
T Consensus 107 ----~~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 107 ----HLID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDA 173 (185)
T ss_pred ----hccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0000 000011112234588899999999999999999 589999999999999999999999999999
Q ss_pred HhCcchhhhh
Q 010092 504 LKHPTRVDYL 513 (518)
Q Consensus 504 LR~~~~~~~L 513 (518)
||+....+.|
T Consensus 174 Lr~~~~~~~~ 183 (185)
T PRK09649 174 LLADAEPDDL 183 (185)
T ss_pred HHhhCCcccc
Confidence 9987665544
No 80
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=99.77 E-value=1.3e-17 Score=153.61 Aligned_cols=157 Identities=14% Similarity=0.194 Sum_probs=121.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFT 352 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~i 352 (518)
+|++.++..|.+.|+.+|+++. ++..+.+|++||+++.+|+++++|++.. .|.+|++..+++.+.+++++ .+..
T Consensus 1 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~ 75 (159)
T TIGR02989 1 EAFAALLQRHQRSLRAFVRSLV---PDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDR 75 (159)
T ss_pred CHHHHHHHHhHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccc
Confidence 3789999999999999999998 7888999999999999999999999764 69999999999999998883 2110
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
.+ .. ++. .+.+.+.
T Consensus 76 -~~---~~---------------------------~~~-----------------------------------~~~~~~~ 89 (159)
T TIGR02989 76 -LV---FD---------------------------DEL-----------------------------------LEALAAE 89 (159)
T ss_pred -cc---cC---------------------------HHH-----------------------------------HHHHHhh
Confidence 00 00 000 0000000
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.++.+..........|..+|+.||++++.||.++| .+++|.+|||+.||+|..+|+...+||+++||..
T Consensus 90 --~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~ 158 (159)
T TIGR02989 90 --AEATEADRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDC 158 (159)
T ss_pred --cccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence 00111122233456789999999999999999988 5899999999999999999999999999999974
No 81
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=99.77 E-value=1.4e-17 Score=166.06 Aligned_cols=178 Identities=16% Similarity=0.155 Sum_probs=136.0
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHH-------HHHhcCCCCCCccchHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT-------AIDRFEPKRRFRLSTYGL 335 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLir-------AvekFDp~rG~kFSTYA~ 335 (518)
..+..+..||..|+..|+..|.+.|+.++.++. ++..+++|++||.|+.+|. ++.+|++. ..|.||++
T Consensus 28 ~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~---~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL~ 102 (244)
T TIGR03001 28 YLACACAQGEPAALAALERHVLSKVPARLAGLR---PPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWVR 102 (244)
T ss_pred HHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHHH
Confidence 455567789999999999999999999999997 6788999999999999994 78889864 36999999
Q ss_pred HHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCcccc
Q 010092 336 FWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSL 414 (518)
Q Consensus 336 ~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SL 414 (518)
..+++.+.++++ +.+...+
T Consensus 103 ~Ia~N~~id~lRk~~r~~~~------------------------------------------------------------ 122 (244)
T TIGR03001 103 IVATRIALELQAQERRHSPV------------------------------------------------------------ 122 (244)
T ss_pred HHHHHHHHHHHHHhcccCcc------------------------------------------------------------
Confidence 999999988887 2110000
Q ss_pred CCCcCCchhhhhcccccCCCCcchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCH
Q 010092 415 HSRHGVTQEEFINGITDVDGVENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISR 490 (518)
Q Consensus 415 D~~~~~~~eel~~~l~d~~~~~~ee~~~~----~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISr 490 (518)
+. .+...+ ..+. ..++++.... .+....|..+|+.||+++|+||.|+| .+++|++|||++||||.
T Consensus 123 ~~-----~~~~~~-~~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~ 191 (244)
T TIGR03001 123 EE-----PTELAA-LPAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHR 191 (244)
T ss_pred cc-----cccccc-ccCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCH
Confidence 00 000000 0001 1122322221 34567799999999999999999999 68999999999999999
Q ss_pred HHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092 491 EMVRKHEVKGLMKLKHPTRVDYLRQH 516 (518)
Q Consensus 491 erVRqie~rALkKLR~~~~~~~L~~y 516 (518)
++|+..+.+|+++||+....+-...|
T Consensus 192 ~TVk~rl~RAr~~Lr~~l~~~~~~~~ 217 (244)
T TIGR03001 192 STVSRWVAQARERLLERTRRRLAERL 217 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999998776655544
No 82
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1e-17 Score=157.03 Aligned_cols=168 Identities=13% Similarity=0.061 Sum_probs=126.6
Q ss_pred HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
..+..||..|++.|+..|.+.|+.++.++. + ..+++|++||+|+.+|+..+.|++. ..|.+|++..+++.+.++
T Consensus 3 ~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~ 76 (175)
T PRK12518 3 LRCQRGDRQSFRQLYRRYQQKVRSTLYQLC---G-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDA 76 (175)
T ss_pred hHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---C-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHH
Confidence 446789999999999999999999999976 3 4689999999999999999999974 369999999999998888
Q ss_pred HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092 346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 425 (518)
Q Consensus 346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel 425 (518)
+++.... +... +. ...
T Consensus 77 ~R~~~~~--~~~~--------------------------------------------------------~~-----~~~- 92 (175)
T PRK12518 77 RRQFAQR--PSRI--------------------------------------------------------QD-----DSL- 92 (175)
T ss_pred HHHhhcc--ccch--------------------------------------------------------hc-----ccc-
Confidence 7621100 0000 00 000
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
... ... ..+++..........+..+|+.||++++.||.|+| .+++|++|||+.||+|..+|++.+.||+++||
T Consensus 93 ~~~-~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~ 165 (175)
T PRK12518 93 NDQ-PSR--PSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLR 165 (175)
T ss_pred ccc-ccC--CCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 000 000 01111122223445688999999999999999998 58999999999999999999999999999999
Q ss_pred Ccchh
Q 010092 506 HPTRV 510 (518)
Q Consensus 506 ~~~~~ 510 (518)
.....
T Consensus 166 ~~l~~ 170 (175)
T PRK12518 166 KFLQQ 170 (175)
T ss_pred HHHHh
Confidence 86543
No 83
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=99.76 E-value=1.9e-17 Score=156.32 Aligned_cols=167 Identities=15% Similarity=0.107 Sum_probs=120.9
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC-----CHHHHHHHHHHHHHH-HHHhcCCCCCCccchHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-----RFQDLCQAGVKGLIT-AIDRFEPKRRFRLSTYGLFWI 338 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~-----~~eDLIQEG~IGLir-AvekFDp~rG~kFSTYA~~wI 338 (518)
+..+..||..|+..|+..|.+.++.+|.+|. ++.. +++|++||+|+.+|+ ...+|++. ..|.+|++.++
T Consensus 8 i~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~ 82 (183)
T TIGR02999 8 LQQWQNGDAAARDQLFPQLYQELRRIARRQL---RRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM 82 (183)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---hcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence 4556789999999999999999999999998 5555 899999999999998 78888754 36999999999
Q ss_pred HHHHHHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCC
Q 010092 339 RHAIIRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417 (518)
Q Consensus 339 RqaI~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~ 417 (518)
++.+.+.+++ .+..+... .....++
T Consensus 83 ~n~~~d~~R~~~~~~~~~~----------------------------------------------------~~~~~~~-- 108 (183)
T TIGR02999 83 RRILVDHARRRRAQKRGGG----------------------------------------------------AVRVPLD-- 108 (183)
T ss_pred HHHHHHHHHHHHHHhccCC----------------------------------------------------ccccccc--
Confidence 9999888762 11000000 0000000
Q ss_pred cCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 497 (518)
Q Consensus 418 ~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie 497 (518)
...... .++. .+.......+...|+.||+++|.||.|+| .+++|++|||+.||+|..+|+..+
T Consensus 109 ----------~~~~~~--~~~~-~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l 171 (183)
T TIGR02999 109 ----------EVLPDA--EADL-DEELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDW 171 (183)
T ss_pred ----------cccCCC--CccH-HHHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 000000 0111 11111122334456779999999999999 589999999999999999999999
Q ss_pred HHHHHHHhCc
Q 010092 498 VKGLMKLKHP 507 (518)
Q Consensus 498 ~rALkKLR~~ 507 (518)
.||+++||+.
T Consensus 172 ~Rar~~Lr~~ 181 (183)
T TIGR02999 172 RFARAWLADE 181 (183)
T ss_pred HHHHHHHHHH
Confidence 9999999964
No 84
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=99.76 E-value=1.8e-17 Score=158.09 Aligned_cols=180 Identities=14% Similarity=0.143 Sum_probs=130.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR 353 (518)
Q Consensus 275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR 353 (518)
+++.|+..|.+.|+.+|.++. ++..+++|++||.|+.+|+.+++|+... .|.+|++..+++.+.++++ +.+...
T Consensus 3 ~~~~l~~~~~~~l~~~a~~~~---~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~ 77 (191)
T PRK12520 3 IAPAQLEALRPHLLRFARLQL---RDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVR 77 (191)
T ss_pred chHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCc
Confidence 689999999999999999998 7788999999999999999999998543 6999999999999999888 322111
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~ 433 (518)
.+..... .....++ ++... +.+.......+ .
T Consensus 78 ~~~~~~~-----------------------~~~~~~~-----------------------~~~~~--~~~~~~~~~~~-~ 108 (191)
T PRK12520 78 LSLDDAD-----------------------EQSDDDL-----------------------FDALF--AADGHYREPPS-D 108 (191)
T ss_pred ccccccc-----------------------cchhhhh-----------------------hhhhc--ccccccccCcc-c
Confidence 1100000 0000000 00000 00000000111 1
Q ss_pred CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
..++++.....+....|..+|..||+++|.||.|+| .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus 109 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 109 WGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 123555555666677899999999999999999999 589999999999999999999999999999998766543
No 85
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=99.75 E-value=6.9e-17 Score=153.27 Aligned_cols=170 Identities=18% Similarity=0.148 Sum_probs=132.5
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r 344 (518)
+.....++..+++.++..|.+.++.++.++. ++..+.+||+||+|+.+|+++..| .. +..|.||++..+++.+.+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD 80 (182)
T COG1595 6 LAEALRGDRAAFEELLERLRPRLRRLARRLL---GDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAID 80 (182)
T ss_pred HHHHHhcchHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHH
Confidence 3445688999999999999999999999999 666699999999999999999999 33 347999999999999999
Q ss_pred HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
.++ +.+.... . . ..
T Consensus 81 ~~R~~~r~~~~-~--~--------------------------------------------------------------~~ 95 (182)
T COG1595 81 RLRKRKRRRAR-V--E--------------------------------------------------------------EA 95 (182)
T ss_pred HHHHhcccccc-c--c--------------------------------------------------------------cc
Confidence 988 3221110 0 0 00
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+......+...... +.....+....|..+|..||+++|.+|.|+| .+++|++|||+.||||.++|+..+++|+.+
T Consensus 96 ~~~~~~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~ 170 (182)
T COG1595 96 DLLPEEADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKK 170 (182)
T ss_pred cccccccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 00000000000000 2345567778899999999999999999999 689999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
|+....
T Consensus 171 l~~~l~ 176 (182)
T COG1595 171 LREQLE 176 (182)
T ss_pred HHHHHh
Confidence 997654
No 86
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=99.75 E-value=4.7e-17 Score=157.83 Aligned_cols=164 Identities=17% Similarity=0.200 Sum_probs=130.5
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
.|+..+++.|+..|.+.++.++.++. ++..+.+|++||+|+.+|+...+|++ + .|.+|++..+++.+.+++++.
T Consensus 24 ~~d~~a~~~l~~~~~~~L~~~~~~~~---~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~ 97 (203)
T PRK09647 24 KATMPSWEELVRQHADRVYRLAYRLS---GNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRR 97 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999999999999 77789999999999999999999985 3 699999999999999988832
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 429 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l 429 (518)
...+.. . ++ +++ +..
T Consensus 98 ~~~~~~----~-----------------------------------------------------~~-------~~~-~~~ 112 (203)
T PRK09647 98 ARIRME----A-----------------------------------------------------LP-------EDY-DRV 112 (203)
T ss_pred ccCccc----c-----------------------------------------------------cc-------ccc-ccc
Confidence 111000 0 00 000 000
Q ss_pred ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
. ....+++.......+...|..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.+.||+++||+...
T Consensus 113 ~-~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 113 P-GDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred C-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 1 11223444455666777899999999999999999998 589999999999999999999999999999997554
No 87
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=5.5e-17 Score=153.53 Aligned_cols=166 Identities=14% Similarity=0.070 Sum_probs=126.8
Q ss_pred HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccC--CCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA--NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345 (518)
Q Consensus 268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~--~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra 345 (518)
...||..++..|+..|.+.|+.++..+. + +..+++|++||.|+.+|+..+.|+......|.||++...++.+.++
T Consensus 7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~---~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~ 83 (178)
T PRK12529 7 CLSADRDKVATLYRENHAWLRNWLAYRL---RSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSW 83 (178)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999876665 3 3568999999999999999999985444579999999999988877
Q ss_pred HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092 346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 425 (518)
Q Consensus 346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel 425 (518)
+++.+ ...... + .+
T Consensus 84 ~Rk~~---------------------~~~~~~-------------------------------------~--------~~ 97 (178)
T PRK12529 84 RRRQS---------------------LELAWL-------------------------------------E--------AL 97 (178)
T ss_pred HHHHH---------------------HHhhhh-------------------------------------h--------Hh
Confidence 66210 000000 0 00
Q ss_pred hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.. .......++++.....+....|..+|..||+++|.||.|+| .+++|++|||+.||+|.++|+..+++|+.+|+
T Consensus 98 ~~-~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 98 AT-LPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred hh-ccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 00 00011123444444555567899999999999999999998 58999999999999999999999999999998
Q ss_pred Cc
Q 010092 506 HP 507 (518)
Q Consensus 506 ~~ 507 (518)
..
T Consensus 173 ~~ 174 (178)
T PRK12529 173 SL 174 (178)
T ss_pred Hh
Confidence 65
No 88
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=99.75 E-value=6.1e-17 Score=158.71 Aligned_cols=169 Identities=14% Similarity=0.089 Sum_probs=130.0
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV- 348 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~- 348 (518)
.....++..|+..|.+.++.++.++. ++..+.+|++||.|+.+|+.+++|++. .|.+|++..+++.+.+++++
T Consensus 14 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~ 87 (216)
T PRK12533 14 AARGERFRQLVLPHLDAAYNLARWLC---GNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRR 87 (216)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhh
Confidence 45578999999999999999999998 778899999999999999999999853 48999999999999888772
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~ 428 (518)
.+...... .+ .++ .+...+.
T Consensus 88 ~~~~~~~~--~~----------------------------------------------------~~~------~~~~~~~ 107 (216)
T PRK12533 88 ANAHEVAA--PD----------------------------------------------------TLD------DADSLDD 107 (216)
T ss_pred cccccccc--cc----------------------------------------------------ccc------ccccccc
Confidence 21100000 00 000 0000000
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
. ++...++++.+...+....|..+|+.||++++.||.|+| .+++|++|||+.||||.++|+++++||+++||+.+
T Consensus 108 ~-~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 108 W-QPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred c-ccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 0 111123555566667778899999999999999999999 58999999999999999999999999999999865
Q ss_pred h
Q 010092 509 R 509 (518)
Q Consensus 509 ~ 509 (518)
.
T Consensus 183 ~ 183 (216)
T PRK12533 183 G 183 (216)
T ss_pred c
Confidence 4
No 89
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=99.74 E-value=5.7e-17 Score=150.15 Aligned_cols=157 Identities=16% Similarity=0.147 Sum_probs=124.2
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s 349 (518)
.|+..+++.|+..|.+.|+.+|..+. ++..+.+|++||+|+.+|++.++|+. ...|.+|++..+++.+.+++++.
T Consensus 2 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~ 76 (162)
T TIGR02983 2 SATEEEFTAFVAARYPRLLRTAYLLT---GDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRR 76 (162)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhh
Confidence 47899999999999999999999998 77889999999999999999999964 34799999999999888877621
Q ss_pred CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 429 (518)
Q Consensus 350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l 429 (518)
....+ . +. +.
T Consensus 77 ~~~~~----------------------------------------------------------~-~~-------~~---- 86 (162)
T TIGR02983 77 RLLEL----------------------------------------------------------P-TR-------EL---- 86 (162)
T ss_pred ccccc----------------------------------------------------------c-cc-------cc----
Confidence 10000 0 00 00
Q ss_pred ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
.... +++..........|..+|..||++++.||.|+| .+++|.+|||+.||+|..+|++.+.||+++||+..
T Consensus 87 ~~~~---~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 87 PDAA---APDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred Cccc---CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 0000 011112334556789999999999999999999 58999999999999999999999999999999754
No 90
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=99.74 E-value=9.5e-17 Score=150.70 Aligned_cols=164 Identities=16% Similarity=0.088 Sum_probs=124.4
Q ss_pred HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV 348 (518)
Q Consensus 269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~ 348 (518)
..|+..|+..|+..|.+.|+.++.++. ++..+++|++||.|+.+|+. ..|... ..|.+|++..+++.+.+++++
T Consensus 5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk 78 (172)
T PRK12523 5 QSPHSELVGALYRDHRGWLLAWLRRNV---ACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRR 78 (172)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999999999998 77889999999999999986 445543 369999999999999988872
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~ 428 (518)
.. + .. ... . ++ ..
T Consensus 79 ~~------------------~--~~-~~~-~---------~~-----------------------------------~~- 91 (172)
T PRK12523 79 AA------------------L--EQ-AYL-A---------EL-----------------------------------AL- 91 (172)
T ss_pred HH------------------H--HH-HHH-H---------HH-----------------------------------hh-
Confidence 10 0 00 000 0 00 00
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
........++......+....|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|++.+.+|+++||..+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 92 VPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred cccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 00000112333333334446799999999999999999998 58999999999999999999999999999998654
Q ss_pred h
Q 010092 509 R 509 (518)
Q Consensus 509 ~ 509 (518)
.
T Consensus 168 ~ 168 (172)
T PRK12523 168 Y 168 (172)
T ss_pred c
Confidence 3
No 91
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=8.1e-17 Score=154.00 Aligned_cols=160 Identities=13% Similarity=0.083 Sum_probs=123.9
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
+|..++..|+..|.+.++.+|.++. ++..+++|++||.|+.+|+..++|+... .|.+|++..+++.+.+++++.+
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~---~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~ 81 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLI---GRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRG 81 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhc
Confidence 5688999999999999999999999 7788999999999999999999998643 5999999999999988887311
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
.. +. . .+ +.+.+..
T Consensus 82 ~~--~~---~-----------------------------------------------------~~-------~~~~~~~- 95 (187)
T PRK12516 82 RE--VQ---D-----------------------------------------------------TD-------GMFTEQL- 95 (187)
T ss_pred CC--cc---c-----------------------------------------------------cc-------ccccccc-
Confidence 00 00 0 00 0000000
Q ss_pred cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
+. .++. ........|..+|..||++++.||.|+| .+++|++|||+.||+|.++|+..+.+|+++||+.+..
T Consensus 96 ~~---~~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 96 AV---HPSQ--YGTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CC---Ccch--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 00 0110 1112235688999999999999999998 5899999999999999999999999999999986654
No 92
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=99.73 E-value=4.6e-17 Score=155.58 Aligned_cols=173 Identities=14% Similarity=0.076 Sum_probs=127.0
Q ss_pred HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-
Q 010092 270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV- 348 (518)
Q Consensus 270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~- 348 (518)
.++..+|+.|+..|.+.|+.+|.++. ++..+++|++||.|+.+|+....|++. ..|.+|++..+++.+.+++++
T Consensus 7 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~ 81 (193)
T TIGR02947 7 TQRAQRFERDALEYLDQLYGAALRMT---RNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKA 81 (193)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999998 677889999999999999999999864 369999999999999988873
Q ss_pred cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092 349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428 (518)
Q Consensus 349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~ 428 (518)
.+..... .. +++. .. .+.. . ..
T Consensus 82 ~~~~~~~---~~---------------------------~~~~-----------~~--------~~~~----~-----~~ 103 (193)
T TIGR02947 82 QRRPQQS---DD---------------------------DDIE-----------DW--------QLAK----A-----AS 103 (193)
T ss_pred cCCcccc---cc---------------------------hhhh-----------hh--------hhcc----c-----cc
Confidence 2110000 00 0000 00 0000 0 00
Q ss_pred cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
........++...........|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus 104 ~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 104 HTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred cccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 00000011222222334456788999999999999999999 68999999999999999999999999999999765
Q ss_pred h
Q 010092 509 R 509 (518)
Q Consensus 509 ~ 509 (518)
.
T Consensus 180 ~ 180 (193)
T TIGR02947 180 V 180 (193)
T ss_pred H
Confidence 4
No 93
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=99.73 E-value=2.7e-16 Score=145.76 Aligned_cols=158 Identities=17% Similarity=0.133 Sum_probs=120.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i 352 (518)
..|++.|+..|.+.|+.++.++. ++..+.+|++||.|+.+|+..+.|++. .|.+|.+.++++.+.++++...
T Consensus 3 ~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~-- 74 (161)
T PRK12528 3 SATVEGLYSAHHHWLTGWLRRRL---GCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQD-- 74 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHc---CCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHH--
Confidence 36899999999999999999999 677899999999999999998887642 5899999999999988876210
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
. ... .. +++ ....+.
T Consensus 75 --------------~---~~~---~~---------~~~------------------------------------~~~~~~ 89 (161)
T PRK12528 75 --------------L---ERA---YL---------EAL------------------------------------AQLPER 89 (161)
T ss_pred --------------H---HHh---hH---------HHh------------------------------------hccccc
Confidence 0 000 00 000 000000
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
....++......+....|..+|..||++++.||.|+| .+++|++|||+.||+|.++|+..+.+|+++||..
T Consensus 90 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 160 (161)
T PRK12528 90 VAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA 160 (161)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence 0111222233334456799999999999999999999 5899999999999999999999999999999854
No 94
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=99.73 E-value=6e-17 Score=149.83 Aligned_cols=154 Identities=14% Similarity=0.090 Sum_probs=119.3
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCcccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE 359 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~ 359 (518)
+.|.+.|+.+|.++. ++..+++|++||+|+.+|++.++|++. .|.+|++..+++.+.+++++ .+....
T Consensus 2 ~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~----- 70 (160)
T PRK09642 2 QTYRHYIFQVIFSIL---RHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE----- 70 (160)
T ss_pred chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc-----
Confidence 568999999999998 778899999999999999999999863 49999999999999988872 210000
Q ss_pred chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 439 (518)
Q Consensus 360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee 439 (518)
.++.. .. .+... ...++++
T Consensus 71 ----------------------------------------------------~~~~~----~~---~~~~~--~~~~~~~ 89 (160)
T PRK09642 71 ----------------------------------------------------LSLCK----ET---EENIK--SSHNIED 89 (160)
T ss_pred ----------------------------------------------------cccch----hh---hhhcc--CCCChHH
Confidence 00000 00 00000 1112344
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
.....+....|..+|+.||+.++.||.|+| .+++|++|||+.||+|..+|++.+.||+++||.....
T Consensus 90 ~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (160)
T PRK09642 90 LLLTKEQKLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE 156 (160)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 455556677899999999999999999999 5899999999999999999999999999999986643
No 95
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2.1e-16 Score=152.35 Aligned_cols=167 Identities=16% Similarity=0.127 Sum_probs=126.4
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.+...|+..|++.|+..|.+.++.++. +. ++..+++|++||.|+.+|+..++|++. ..|.+|++..+++.+.
T Consensus 15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~---~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~i 88 (196)
T PRK12535 15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HL---GGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWV 88 (196)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHH
Confidence 35567789999999999999999999975 45 577899999999999999999999864 3699999999999999
Q ss_pred HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
+++++ .+..+.. . +. .
T Consensus 89 d~~Rk~~~~~~~~----~------------------------------------------------------~~-----~ 105 (196)
T PRK12535 89 DNIRHDMARPRKS----A------------------------------------------------------TE-----Y 105 (196)
T ss_pred HHHHhhccCCCcc----c------------------------------------------------------cc-----c
Confidence 88883 2110000 0 00 0
Q ss_pred hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
... .+ ....++... .......|..+|+.||+++++||.|+| .+++|++|||+.||+|..+|++.++||++
T Consensus 106 ~~~----~~-~~~~~~~~~-~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 106 EDA----AA-TTASNETTG-SWSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred ccc----cc-ccCCcchhH-HHHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 000 00 000111111 112234788999999999999999999 68999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||+.+.
T Consensus 176 ~Lr~~l~ 182 (196)
T PRK12535 176 DLIAATA 182 (196)
T ss_pred HHHHHhc
Confidence 9997543
No 96
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=99.72 E-value=2e-16 Score=146.64 Aligned_cols=158 Identities=15% Similarity=0.059 Sum_probs=120.5
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
++..|+..++..|.+.|+.++.++. ++..+++|++||+++.+|+..++|++. .|.||++..+++.+.+++++.+
T Consensus 2 ~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~ 75 (161)
T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLT---GDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEK 75 (161)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcc
Confidence 4578999999999999999999998 778899999999999999999999863 5999999999999998887311
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
.. ... . . ++.. .
T Consensus 76 ~~-~~~---~-----------------------------------------------------~--------~~~~-~-- 87 (161)
T PRK12541 76 KY-KTT---T-----------------------------------------------------I--------EEFH-L-- 87 (161)
T ss_pred cc-ccc---c-----------------------------------------------------h--------hhhh-c--
Confidence 00 000 0 0 0000 0
Q ss_pred cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
+.....+++.....+. ..+..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus 88 ~~~~~~~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 88 PNVPSTEHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred cCCCCcHHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 0000001122222222 3455789999999999999999 5899999999999999999999999999999964
No 97
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=99.72 E-value=2.2e-16 Score=146.61 Aligned_cols=158 Identities=14% Similarity=0.091 Sum_probs=123.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC-C
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-F 351 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr-~ 351 (518)
..+++.|+..|.+.|+.+|.++. ++..+++|++||+|+.+|++ .|+. +..|.+|++..+++.+.++++..+ .
T Consensus 2 ~~~f~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~ 74 (166)
T PRK09639 2 DETFEDLFEQYYPDVVQQIFYIV---KDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRR 74 (166)
T ss_pred chHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccc
Confidence 46899999999999999999998 77889999999999999999 6764 347999999999999998887311 0
Q ss_pred ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092 352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431 (518)
Q Consensus 352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d 431 (518)
.+... . ..+..+ +
T Consensus 75 ~~~~~---~-------------------------------------------------------------~~~~~~-~-- 87 (166)
T PRK09639 75 RARIL---G-------------------------------------------------------------EFQWQE-V-- 87 (166)
T ss_pred ccccc---c-------------------------------------------------------------hhhhhh-c--
Confidence 00000 0 000000 0
Q ss_pred CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
+....+++.....+....|..+|..||++++.||.++| +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus 88 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 88 DNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred cCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 11223455555556667789999999999999999999 58999999999999999999999999999998654
No 98
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.71 E-value=2.9e-16 Score=161.52 Aligned_cols=182 Identities=17% Similarity=0.110 Sum_probs=129.2
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
||..|++.|+..|.+.++.+|.++. ++..+.+|++||.|+.+|+...+|+.. ..|.+|++..+++.+.+++++.+
T Consensus 2 gd~~af~~l~~~~~~~l~~~a~~~~---~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~ 76 (324)
T TIGR02960 2 VDGAAFTALAEPHRRELLAHCYRML---GSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQ 76 (324)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHhc---CChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhcc
Confidence 6789999999999999999999998 778899999999999999999999864 36999999999999999888321
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
....+. .. .. ..................+.+.
T Consensus 77 ~~~~~~--~~--------------------~~--------------------------~~~~~~~~~~~~~~~~~~~~~~ 108 (324)
T TIGR02960 77 RRPRPV--GL--------------------GA--------------------------PSADGTAAASEAAEVTWLEPLP 108 (324)
T ss_pred CCcCcc--cc--------------------CC--------------------------CCCcccccccccccccccCCCC
Confidence 100000 00 00 0000000000000000000000
Q ss_pred -------cCCCCcchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 431 -------DVDGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 431 -------d~~~~~~ee~~~~~~-l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.....++++.....+ +...+..+|+.||+++|.||.|+| .+++|++|||+.||+|..+|+++++||++
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 109 DLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARA 184 (324)
T ss_pred ccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 011123444333333 456788999999999999999999 58999999999999999999999999999
Q ss_pred HHhCcch
Q 010092 503 KLKHPTR 509 (518)
Q Consensus 503 KLR~~~~ 509 (518)
+||+...
T Consensus 185 ~Lr~~l~ 191 (324)
T TIGR02960 185 TLDEVGP 191 (324)
T ss_pred HHHHhcc
Confidence 9998654
No 99
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.71 E-value=3e-16 Score=162.76 Aligned_cols=188 Identities=18% Similarity=0.175 Sum_probs=133.8
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
+.+.++..||..|++.|+..|.+.|+.+|.++. ++..+.+|++||.|+.+|+.+++|++. ..|.+|++...++.+
T Consensus 8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~---~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~ 82 (339)
T PRK08241 8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRML---GSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVC 82 (339)
T ss_pred HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHH
Confidence 456678899999999999999999999999998 677899999999999999999999853 369999999999999
Q ss_pred HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092 343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 422 (518)
Q Consensus 343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ 422 (518)
.+++++.+....+..... +..++. . .+. ....
T Consensus 83 ~d~~Rk~~~~~~~~~~~~------------------------~~~~~~-------------------~--~~~---~~~~ 114 (339)
T PRK08241 83 LDALEGRARRPLPTDLGA------------------------PAADPV-------------------D--ELV---ERPE 114 (339)
T ss_pred HHHHHhhccccCccccCC------------------------CcCccc-------------------c--ccc---cccc
Confidence 988873111000000000 000000 0 000 0000
Q ss_pred hhhhcccccC----CCCcchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092 423 EEFINGITDV----DGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 497 (518)
Q Consensus 423 eel~~~l~d~----~~~~~ee~~~~~~-l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie 497 (518)
....+.+.+. ...++++.....+ +...|..+|+.||+++|.||.|+| .+++|++|||+.||+|..+|++.+
T Consensus 115 ~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l 190 (339)
T PRK08241 115 VPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSAL 190 (339)
T ss_pred ccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHH
Confidence 0001111110 0123444333333 455688999999999999999999 589999999999999999999999
Q ss_pred HHHHHHHhCc
Q 010092 498 VKGLMKLKHP 507 (518)
Q Consensus 498 ~rALkKLR~~ 507 (518)
.||+++||+.
T Consensus 191 ~RAr~~Lr~~ 200 (339)
T PRK08241 191 QRARATLAER 200 (339)
T ss_pred HHHHHHHhhc
Confidence 9999999983
No 100
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=99.71 E-value=2.1e-16 Score=147.22 Aligned_cols=155 Identities=15% Similarity=0.113 Sum_probs=123.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc-CCccc
Q 010092 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS-SFTRV 354 (518)
Q Consensus 276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s-r~iRl 354 (518)
++.|+..|.+.|+.+|.++. ++..+++|++||.|+.+|++++.|++. .|.+|++..+++.+.+++++. +...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~ 76 (165)
T PRK09644 3 IEEIYKMYINDVYRYLFSLT---KSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV 76 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc
Confidence 67899999999999999998 778899999999999999999999863 599999999999999888731 10000
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
+.++ .+.+..
T Consensus 77 -------------------------------~~~~------------------------------------~~~~~~--- 86 (165)
T PRK09644 77 -------------------------------GTDE------------------------------------IEAIQA--- 86 (165)
T ss_pred -------------------------------chhH------------------------------------Hhhhcc---
Confidence 0000 000000
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
.++++.....+....|..+|..||+++++||.++| .+++|++|||+.||+|..+|+..+.||+++||+....
T Consensus 87 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 87 ESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred cChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 12344444555667899999999999999999998 5899999999999999999999999999999986543
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=3e-16 Score=146.37 Aligned_cols=156 Identities=12% Similarity=0.046 Sum_probs=121.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCC
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSF 351 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~ 351 (518)
...+..++..|.+.|+.+|.++. ++..+++|++||+|+.+|+..+.|++.. .|.+|++..+++.+.+.++. .+.
T Consensus 5 ~~~f~~~~~~~~~~l~~~a~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~ 79 (164)
T PRK12547 5 SKNFKQELLLALPALRAFAVSLS---SKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGRE 79 (164)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccc
Confidence 56899999999999999999998 7888999999999999999999998543 59999999999999988872 110
Q ss_pred ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092 352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431 (518)
Q Consensus 352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d 431 (518)
+.. .. ...... .+
T Consensus 80 ---~~~-~~--------------------------------------------------------------~~~~~~-~~ 92 (164)
T PRK12547 80 ---VQD-SD--------------------------------------------------------------GVFTAR-VA 92 (164)
T ss_pred ---ccc-cc--------------------------------------------------------------cccccc-CC
Confidence 000 00 000000 00
Q ss_pred CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..++. ........|..+|..||+++++||.|+| .+++|++|||+.||+|..+|++.+.||+++||....
T Consensus 93 ---~~~~~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 161 (164)
T PRK12547 93 ---VHPAQ--YGSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred ---CCchh--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 00111 1122345688999999999999999998 589999999999999999999999999999997654
No 102
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=99.71 E-value=2.9e-16 Score=150.30 Aligned_cols=180 Identities=14% Similarity=0.114 Sum_probs=126.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCC-HHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccc
Q 010092 277 NKLIKHNLRLVLFVIKKYFQDFANGPR-FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV 354 (518)
Q Consensus 277 e~LI~~nlrLV~siAkky~~~~~~g~~-~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRl 354 (518)
+..+..|.+.|+.+|.++. ++..+ ++|++||+|+.+|++.++|+.. ..|.+|++..+++.+.+++++ .+....
T Consensus 8 ~~~~~~~~~~l~~~a~~~~---~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~ 82 (195)
T PRK12532 8 DAELIESRKLLLHFARLQL---PDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKV 82 (195)
T ss_pred hhhHHHHHHHHHHHHHHHc---CChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 3566778999999999998 66777 9999999999999999999864 379999999999999998883 221100
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
...... ....+.. .+.... +............
T Consensus 83 ~~~~~~------------------------~~~~~~~--------------------~~~~~~----~~~~~~~~~~~~~ 114 (195)
T PRK12532 83 FTLLDD------------------------ELLDEAF--------------------ESHFSQ----NGHWTPEGQPQHW 114 (195)
T ss_pred cccccc------------------------cccchhh--------------------hhhhcc----ccccccccCcccc
Confidence 000000 0000000 000000 0000000000111
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L 513 (518)
.++++.....+....+..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++||+......+
T Consensus 115 ~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 115 NTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 23555555666777899999999999999999998 5899999999999999999999999999999987765543
No 103
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=3.9e-16 Score=150.76 Aligned_cols=177 Identities=12% Similarity=0.070 Sum_probs=123.0
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG 357 (518)
Q Consensus 279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~ 357 (518)
++..|.+.++.+|.++. ++..+++|++||.|+.+|+..++|++.. .|.+|++..+++.+.++++ +.+...++..
T Consensus 13 ~~~~~~~~l~~~~~~~~---~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~ 87 (201)
T PRK12545 13 YLAQLRHDLLRFARLQL---RDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL 87 (201)
T ss_pred HHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence 47889999999999999 7778999999999999999999999753 6999999999999999888 3221101000
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcc
Q 010092 358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437 (518)
Q Consensus 358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ 437 (518)
.. ++. .. ..++.........+......+...++
T Consensus 88 -~~----------------------------~~~------~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~ 120 (201)
T PRK12545 88 -DA----------------------------ELD------GE------------ALLDRELFKDNGHWAAHAKPRPWPKP 120 (201)
T ss_pred -cc----------------------------ccc------hh------------hhhhhhhhcccccccccccCcCCCCH
Confidence 00 000 00 00000000000000000001111223
Q ss_pred hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 438 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 438 ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
++.....+....|..+|..||+++|.||.|+| .+++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus 121 ~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~ 190 (201)
T PRK12545 121 ETILQQQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK 190 (201)
T ss_pred HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444455566789999999999999999999 58999999999999999999999999999999876543
No 104
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.70 E-value=4.5e-16 Score=148.78 Aligned_cols=178 Identities=15% Similarity=0.124 Sum_probs=127.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (518)
Q Consensus 277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP 355 (518)
.+.+..|.+.|+.+|.++. ++..+++|++||+|+.+|+..+.|++. .+|.+|++..+++.+.++++ +.+....+
T Consensus 5 ~~~~~~~~~~l~~~~~~~~---~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~ 79 (188)
T TIGR02943 5 PQELEQLRRDLLRFARLQL---RDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVS 79 (188)
T ss_pred HHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcc
Confidence 3567789999999999999 778899999999999999999999865 37999999999999999888 32211111
Q ss_pred ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCC
Q 010092 356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435 (518)
Q Consensus 356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~ 435 (518)
. +.. +. ... .++... .+.+............
T Consensus 80 ~-~~~----------------------------~~------~~~-------------~~~~~~-~~~~~~~~~~~~~~~~ 110 (188)
T TIGR02943 80 D-LDD----------------------------EL------DDE-------------AFNALF-TQNGHWAQHGQPQHWN 110 (188)
T ss_pred c-ccc----------------------------cc------ccc-------------hhhhhh-ccccchhccccccccC
Confidence 0 000 00 000 000000 0000000001111112
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
.++..+...+....|..+|..||++++.||.++| .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus 111 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 111 TPEKQLENKEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455556666677899999999999999999998 589999999999999999999999999999998766443
No 105
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=99.70 E-value=4.5e-16 Score=148.81 Aligned_cols=174 Identities=15% Similarity=0.088 Sum_probs=123.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092 277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP 355 (518)
Q Consensus 277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP 355 (518)
+..|..|.+.++.+|.++. ++..+++|++||.|+.+|+..+.|++.. +|.+|++...++.+.++++ +.+.....
T Consensus 10 ~~~~~~~~~~l~~~~~~~~---~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~ 84 (189)
T PRK12530 10 SLEIEEIRLQMLKFATLQL---KDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES 84 (189)
T ss_pred HHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence 3456778889999999998 6778999999999999999999998653 6999999999999998888 32211000
Q ss_pred ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCC
Q 010092 356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435 (518)
Q Consensus 356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~ 435 (518)
.... + .......... .....+........
T Consensus 85 -~~~~----------------------------~-------------------~~~~~~~~~~---~~~~~~~~~~~~~~ 113 (189)
T PRK12530 85 -ELIE----------------------------E-------------------DSPNSFFDEK---GHWKPEYYEPSEWQ 113 (189)
T ss_pred -cccc----------------------------c-------------------ccchhhhccc---ccccccccCCcccc
Confidence 0000 0 0000000000 00000000011112
Q ss_pred cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
++++.....+....|..+|+.||+++|+||.|+| .+++|++|||+.||+|.++|+..++||+++||+.+..
T Consensus 114 ~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 184 (189)
T PRK12530 114 EVENTVYKEEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSK 184 (189)
T ss_pred CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555567777899999999999999999999 5899999999999999999999999999999986543
No 106
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=99.69 E-value=6.2e-16 Score=150.32 Aligned_cols=181 Identities=13% Similarity=0.136 Sum_probs=128.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccc
Q 010092 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV 354 (518)
Q Consensus 276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRl 354 (518)
-..++..|.+.|+.+|.++. ++..+++|++||+|+.+|+.+..|+.. .+|.+|++..+++.+.++++ ..+....
T Consensus 20 ~~~~~~~~~~~l~~~~~~~~---~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~ 94 (206)
T PRK12544 20 DPVFLEDLRKQMIKFATLQL---SDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSA 94 (206)
T ss_pred hHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence 46788999999999999999 788899999999999999999999864 36999999999999999998 3321111
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
+..... ... ...+..+... .............
T Consensus 95 ~~~~~~-------------------------~~~---------~~~~~~~~~~--------------~~~~~~~~~~~~~ 126 (206)
T PRK12544 95 SSLLRD-------------------------EEE---------EEDFEELFDE--------------SGHWQKDERPQAW 126 (206)
T ss_pred cccccc-------------------------cch---------hhHHHHhhcc--------------ccccccccccccc
Confidence 100000 000 0000000000 0000000001111
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L 513 (518)
..+++.....+....+..+|..||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++||+....+.+
T Consensus 127 ~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~ 201 (206)
T PRK12544 127 GNPEESLEQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF 201 (206)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 23455555566667889999999999999999999 5899999999999999999999999999999987765443
No 107
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=99.68 E-value=2.5e-16 Score=144.28 Aligned_cols=150 Identities=15% Similarity=0.083 Sum_probs=116.0
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE 359 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~ 359 (518)
..|.+.|+.++.++. ++..+++|++||+++.+|+++++|++ .+|.+|++..+++.+.++++ +.+....
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~----- 70 (154)
T TIGR02950 2 REYMHDVFRYLYRLT---KDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTI----- 70 (154)
T ss_pred chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccc-----
Confidence 568999999999998 67789999999999999999999997 37999999999999988887 2110000
Q ss_pred chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 439 (518)
Q Consensus 360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee 439 (518)
. .+ .+.+... +....+++
T Consensus 71 ~---------------------------~~----------------------------------~~~~~~~-~~~~~~~~ 88 (154)
T TIGR02950 71 D---------------------------DD----------------------------------AIGDLEQ-HPVESPEH 88 (154)
T ss_pred c---------------------------Hh----------------------------------hhhhccc-cccCChhH
Confidence 0 00 0000000 01112344
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.....+....|..+|+.||+.++.||.++| .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus 89 ~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 89 HLLIKIEQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred HHHHHHHHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444455667799999999999999999998 4899999999999999999999999999999964
No 108
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=99.68 E-value=1.2e-15 Score=145.00 Aligned_cols=152 Identities=16% Similarity=0.152 Sum_probs=121.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC-Cccc
Q 010092 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-FTRV 354 (518)
Q Consensus 276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr-~iRl 354 (518)
++.|+..|.+.|+.+|.++. ++..+++|++||.++.+|+.+..|++. ..|.+|++..+++.+.+++++.+ ...+
T Consensus 3 ~~~l~~~y~~~l~~~~~~~~---~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~ 77 (181)
T PRK09637 3 LESIWSEYKAQLKAFLHSRV---SNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEEL 77 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCc
Confidence 67899999999999999998 788999999999999999999999853 37999999999999998887321 1000
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
+ .+.. ..+
T Consensus 78 ~------------------------------------------------------------------~~~~---~~~--- 85 (181)
T PRK09637 78 P------------------------------------------------------------------DDLL---FED--- 85 (181)
T ss_pred c------------------------------------------------------------------hhhh---ccC---
Confidence 0 0000 000
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.+++.....+....+..+|+.||++++.||.|+| .+++++.|||+.||+|..+|+..+.||+++||+...
T Consensus 86 -~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 86 -EEREENAKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred -CChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 0111223344567899999999999999999998 589999999999999999999999999999997544
No 109
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=1.4e-15 Score=144.83 Aligned_cols=158 Identities=14% Similarity=0.091 Sum_probs=121.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFT 352 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~i 352 (518)
.++..++..|.+.|+.+|.++. ++..+++|++||.|+.+|+..++|++.. .|.+|++..+++.+.+.+++ .+..
T Consensus 5 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~ 79 (182)
T PRK12540 5 DSLRDDILAAVPSLRAFAISLS---GNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREV 79 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccc
Confidence 5678899999999999999998 7788999999999999999999998654 68999999999998887762 1100
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
.. . .+...+.. +.
T Consensus 80 --~~--~--------------------------------------------------------------~~~~~~~~-~~ 92 (182)
T PRK12540 80 --ED--A--------------------------------------------------------------DGSYAKTL-KS 92 (182)
T ss_pred --cc--c--------------------------------------------------------------cccccccc-cC
Confidence 00 0 00000000 00
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
.++.. .......|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|++.++||+++||+.+....
T Consensus 93 ---~~~~~--~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 93 ---QPGQN--AHLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred ---CCchH--HHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 01111 112234689999999999999999999 589999999999999999999999999999998766544
No 110
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=99.67 E-value=1.5e-15 Score=140.76 Aligned_cols=156 Identities=14% Similarity=0.127 Sum_probs=117.5
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF 356 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~ 356 (518)
.++..|.+.++.+|.++. ++..+++|++||+++.+|+....|++. .|.+|++..+++.+.++++ +..... .
T Consensus 2 ~~~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~--~ 73 (163)
T PRK07037 2 DVFVDNRSMLVKIAARIV---GCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK--Y 73 (163)
T ss_pred hHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc--c
Confidence 367788999999999998 778899999999999999988877653 4789999999998888887 211000 0
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCc
Q 010092 357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE 436 (518)
Q Consensus 357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~ 436 (518)
+ ...+.... .... ..+
T Consensus 74 --------------------------------------------------------~------~~~~~~~~-~~~~-~~~ 89 (163)
T PRK07037 74 --------------------------------------------------------H------GDEEDGLD-VPSP-EAS 89 (163)
T ss_pred --------------------------------------------------------c------cccccccc-cCCC-CCC
Confidence 0 00000000 0011 122
Q ss_pred chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
++......+..+.|..+|+.|||+++.||.++| .+++|.+|||+.||+|..+|++.+.+|+++||....
T Consensus 90 ~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~ 158 (163)
T PRK07037 90 PEAALINRDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLD 158 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 444444555667789999999999999999998 589999999999999999999999999999997543
No 111
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=99.67 E-value=2.1e-15 Score=144.23 Aligned_cols=162 Identities=14% Similarity=0.132 Sum_probs=122.8
Q ss_pred HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (518)
Q Consensus 268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~ 347 (518)
-..++..+++.++..|.+.|+.+|.++. ++..+++|++||.|+.+|+.+..|++.. .|.+|++..+++.+.+..+
T Consensus 17 ~~~~~~~~f~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r 91 (188)
T PRK12517 17 DMLSKQRRYEALVKALHADIYRYAYWLC---KDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFE 91 (188)
T ss_pred hhhccHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999999999999 7888999999999999999999998653 6899998888886544333
Q ss_pred hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhc
Q 010092 348 VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 427 (518)
Q Consensus 348 ~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~ 427 (518)
+... ...+.+ ..
T Consensus 92 ~~~~----------------------------------------------------------~~~~~~------~~---- 103 (188)
T PRK12517 92 RKQF----------------------------------------------------------DLVDIE------DD---- 103 (188)
T ss_pred Hhcc----------------------------------------------------------CccCcc------cc----
Confidence 1000 000000 00
Q ss_pred ccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 428 ~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
...+....+++. ......|..+|..||++++.||.++| .+++|++|||+.||+|..+|+..+.||+++||..
T Consensus 104 ~~~~~~~~~~e~----~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (188)
T PRK12517 104 SIEDDASHSSEE----EMEQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA 175 (188)
T ss_pred cccCccccChhH----HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 000110111221 22335689999999999999999999 5899999999999999999999999999999986
Q ss_pred chh
Q 010092 508 TRV 510 (518)
Q Consensus 508 ~~~ 510 (518)
...
T Consensus 176 l~~ 178 (188)
T PRK12517 176 LEK 178 (188)
T ss_pred HHH
Confidence 653
No 112
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=99.66 E-value=4.4e-15 Score=139.67 Aligned_cols=160 Identities=14% Similarity=0.094 Sum_probs=120.1
Q ss_pred HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
.+..|++.++..|.+.++.++.++. ++..+++||+||.|+.+|+. ..|++-. .|.+|++..+++.+.+++++..
T Consensus 7 ~~~~af~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~ 80 (172)
T PRK09651 7 TASLTFESLYGTHHGWLKSWLTRKL---QSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA 80 (172)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999998 77889999999999999987 3454332 5889999888888887776210
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
+ ..... +.+ . .+.
T Consensus 81 ------------------~-~~~~~------------~~~--------------------------------~----~~~ 93 (172)
T PRK09651 81 ------------------L-EKAYL------------EML--------------------------------A----LMP 93 (172)
T ss_pred ------------------H-Hhhhh------------hHH--------------------------------h----hcc
Confidence 0 00000 000 0 000
Q ss_pred cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
+....+++......+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|+..++||+++|+..
T Consensus 94 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 94 EGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred ccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 001112333333344556789999999999999999999 5899999999999999999999999999999854
No 113
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=99.66 E-value=1.7e-15 Score=142.42 Aligned_cols=147 Identities=17% Similarity=0.152 Sum_probs=115.6
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCcccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE 359 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~ 359 (518)
..|.+.++.++.++. ++..+++|++||+|+.+|+++..|++. .+|.+|++..+++.+.++++. .+...++
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~---- 72 (170)
T TIGR02959 2 DEFRSELKAFIKSRV---SDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP---- 72 (170)
T ss_pred chHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc----
Confidence 457888999999998 788899999999999999999999963 479999999999999998883 2110000
Q ss_pred chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 439 (518)
Q Consensus 360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee 439 (518)
+... ... ++++
T Consensus 73 ---------------------------------------------------------------~~~~----~~~--~~~~ 83 (170)
T TIGR02959 73 ---------------------------------------------------------------ESLL----AAD--SARE 83 (170)
T ss_pred ---------------------------------------------------------------hhhc----ccC--CccH
Confidence 0000 000 1112
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.....+....|..+|..||++++.||.++| .+++|++|||+.||+|..+|++.+.||+++||....
T Consensus 84 ~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 84 ETFVKELSQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 223344566799999999999999999998 589999999999999999999999999999997543
No 114
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=99.66 E-value=1.4e-15 Score=140.62 Aligned_cols=153 Identities=13% Similarity=0.103 Sum_probs=116.5
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLES 360 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e 360 (518)
..|.+.++.++.++. ++..+++|++||.|+.+|+..+.|++. +|.||++..+++.+.++++......
T Consensus 2 ~~~~~~l~~~~~~~~---~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~------- 68 (159)
T PRK12527 2 ENYYRELVRFLSARL---GNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQ------- 68 (159)
T ss_pred hhHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccc-------
Confidence 467888889999998 677889999999999999999998753 6899999999999988877211000
Q ss_pred hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhh
Q 010092 361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 440 (518)
Q Consensus 361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~ 440 (518)
. .+++. +.+. ......++++.
T Consensus 69 ---------------~-----------------------------------~~~~~--------~~~~-~~~~~~~~~~~ 89 (159)
T PRK12527 69 ---------------A-----------------------------------EPLEV--------LDEE-ERLHSPSPQTR 89 (159)
T ss_pred ---------------c-----------------------------------cchhh--------hhcc-ccccCCCHHHH
Confidence 0 00000 0000 00011234555
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 441 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 441 ~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
....+....|..+|..||++++.||.|+| .+++|++|||+.||+|.++|+..+.||+++||....
T Consensus 90 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 90 LDLGQRLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55556667899999999999999999999 589999999999999999999999999999997654
No 115
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=99.65 E-value=4.1e-15 Score=142.54 Aligned_cols=157 Identities=12% Similarity=0.075 Sum_probs=117.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i 352 (518)
..+++.|.. |.+.|+++|..+. ++..+++|++||.|+.+|+.+..|+.. ..|.+|++..+++.+.+++++...
T Consensus 7 ~~~~~~l~~-~~~~l~~~a~~~l---~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r- 79 (188)
T PRK12546 7 RDPRDELVE-HLPALRAFAISLT---RNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKR- 79 (188)
T ss_pred hhHHHHHHH-HHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcc-
Confidence 456667766 6799999999998 788999999999999999999999864 369999999999999887773110
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
.+. . .+ +...+...++
T Consensus 80 -~~~---~-----------------------------------------------------~~-------~~~~~~~~~~ 95 (188)
T PRK12546 80 -EVP---D-----------------------------------------------------PE-------GVHAASLAVK 95 (188)
T ss_pred -ccc---C-----------------------------------------------------cc-------cccccccccC
Confidence 000 0 00 0000000000
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
+.. ........+..+|+.||++++.||.|+| .+++|.+|||+.||+|..+|++.+.||+++||+....
T Consensus 96 ----~~~--~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 96 ----PAH--DGRLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred ----Ccc--hhHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 000 1122235688999999999999999998 5899999999999999999999999999999976543
No 116
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=99.64 E-value=1.5e-14 Score=135.37 Aligned_cols=159 Identities=14% Similarity=0.076 Sum_probs=120.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352 (518)
Q Consensus 273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i 352 (518)
..++.+++..|.+.++.+|.++. ++..+.+|++||.|+.+|+..+.++. ..|.+|++..+++.+.++++..+
T Consensus 8 ~~~~~~~~~~~~~~l~~~~~~~~---~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~-- 79 (168)
T PRK12525 8 NTLIGQMFQQDYDWLCKKLSRQL---GCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQD-- 79 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc---CCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHH--
Confidence 46889999999999999999998 67789999999999999986555542 26899999888888887766210
Q ss_pred cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092 353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV 432 (518)
Q Consensus 353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~ 432 (518)
..+. .... + .+ ....
T Consensus 80 -----------------~~~~---~~~~---------------------------------~-----------~~-~~~~ 94 (168)
T PRK12525 80 -----------------LERA---YLQS---------------------------------L-----------AE-APEA 94 (168)
T ss_pred -----------------HHHH---HHHH---------------------------------H-----------hc-cccc
Confidence 0000 0000 0 00 0000
Q ss_pred CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
...++++..........|..+|+.||++++.||.|+| .+++|++|||+.||+|..+|+..+.+|+++|+...
T Consensus 95 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~ 166 (168)
T PRK12525 95 VQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF 166 (168)
T ss_pred ccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence 1122444444555667899999999999999999998 58999999999999999999999999999999653
No 117
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=99.63 E-value=9.3e-15 Score=139.31 Aligned_cols=154 Identities=12% Similarity=0.091 Sum_probs=116.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccc
Q 010092 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV 354 (518)
Q Consensus 276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRl 354 (518)
....+..+++.|+.+|.++. ++..+.+|++||.|+.+|+....|+... .|.+|++..+++.+.+++++ .+....
T Consensus 6 ~~~~~~~~~~~l~~~~~~~~---~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~ 80 (182)
T PRK12511 6 KRFDVLDQLVPLRRYARSLT---RDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARR 80 (182)
T ss_pred hhhhHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhcccccc
Confidence 34457788999999999998 7788999999999999999999998643 69999999999999988873 111000
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
.+++ .. ..+...
T Consensus 81 --------------------------------~~~~--------------------------------~~----~~~~~~ 92 (182)
T PRK12511 81 --------------------------------ADEL--------------------------------AV----LADASL 92 (182)
T ss_pred --------------------------------ccch--------------------------------hh----ccccCC
Confidence 0000 00 000000
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..+. ........|..+|..||++++.||.|+| .+++|++|||+.||+|.++|++.+.||+++||....
T Consensus 93 ~~~~---~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 93 PAAQ---EHAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred Ccch---HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 0011 1122345688999999999999999998 589999999999999999999999999999997543
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.60 E-value=1.4e-14 Score=147.76 Aligned_cols=159 Identities=15% Similarity=0.051 Sum_probs=118.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR 353 (518)
.....++..|.+.++.+|+++. ++..+++|++||.|+. |.....|+. ..|.+|++..+++.+.+++++.+..+
T Consensus 4 ~~~~~l~~~~~~~l~~~a~~~~---~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~ 76 (293)
T PRK09636 4 ADAAAEFEPLRPHLLSVAYRML---GSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR 76 (293)
T ss_pred cHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc
Confidence 4577899999999999999998 7788999999999999 556677752 46999999999999988887211000
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~ 433 (518)
... . .. .+. +...+..
T Consensus 77 -~~~--~------------------------------------------------~~--~~~-----------e~~~~~~ 92 (293)
T PRK09636 77 -ETY--V------------------------------------------------GP--WLP-----------EPVVEEL 92 (293)
T ss_pred -ccc--c------------------------------------------------CC--cCC-----------cCCCCCC
Confidence 000 0 00 000 0001111
Q ss_pred CCcchh-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 434 GVENEN-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 434 ~~~~ee-~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
.++++ ......+...+..+|+.|||++|.||.|+| ..++|++|||+.||+|..+|++.++||+++||+..
T Consensus 93 -~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 93 -DDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred -CChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 11322 233445566789999999999999999999 58999999999999999999999999999999853
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=99.59 E-value=1.5e-14 Score=133.38 Aligned_cols=152 Identities=11% Similarity=0.078 Sum_probs=105.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccccccccchhhHHHHHHHHHHHHHH
Q 010092 299 ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLEL 377 (518)
Q Consensus 299 ~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL 377 (518)
++..+++|++||+|+.+|+....+ + +..|.+|++..+++.+.+++++ .+.......
T Consensus 2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~-------------------- 58 (161)
T PRK09047 2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL-------------------- 58 (161)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence 345679999999999999988863 3 3469999999999999998873 211000000
Q ss_pred HHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC--CCcchhhhHHHHHHHHHHHHHh
Q 010092 378 LFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD--GVENENQRQPALLRLALDDVLD 455 (518)
Q Consensus 378 ~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~--~~~~ee~~~~~~l~~~L~~~L~ 455 (518)
..++......+..+..+.+.+.. ..++++.....+....|..+|.
T Consensus 59 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~ 105 (161)
T PRK09047 59 ---------------------------------FSSFSDDDDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQ 105 (161)
T ss_pred ---------------------------------ccccccccccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHH
Confidence 00000000000011111111111 1235555666677788999999
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
.||++++.||.|+| .+++|++|||+.||+|..+|+..+.+|+++||.....
T Consensus 106 ~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 106 KLPARQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred hCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999 5899999999999999999999999999999976654
No 120
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=99.56 E-value=6.1e-14 Score=138.70 Aligned_cols=158 Identities=18% Similarity=0.119 Sum_probs=119.7
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII 343 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ 343 (518)
.+.+...++..+++.+++.| +.++.+|.++. ++..+.+||+||.|+.+|+. |+.. ..|.+|++...++.+.
T Consensus 8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~---~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~i 78 (228)
T PRK06704 8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLT---KNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWL 78 (228)
T ss_pred HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHH
Confidence 46667788899999888888 78999999998 77889999999999999986 5543 2489999999999888
Q ss_pred HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092 344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423 (518)
Q Consensus 344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e 423 (518)
+.+++.... . .+ .+.
T Consensus 79 d~~Rk~k~~-------~---------------~~------------------------------------~~~------- 93 (228)
T PRK06704 79 DQIKSKSVH-------E---------------KI------------------------------------RDQ------- 93 (228)
T ss_pred HHHhccccc-------c---------------cc------------------------------------ccc-------
Confidence 877621100 0 00 000
Q ss_pred hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
.... .+++. .......+..+|+.||+++|.||.|+| .+++|++|||+.||+|.++|++.+.||+++
T Consensus 94 -----~~~~---~~~~~--~~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~ 159 (228)
T PRK06704 94 -----ITFE---EPHEK--IADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNR 159 (228)
T ss_pred -----cccC---ChHHH--HHHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 0000 01111 122345688999999999999999998 589999999999999999999999999999
Q ss_pred HhCcch
Q 010092 504 LKHPTR 509 (518)
Q Consensus 504 LR~~~~ 509 (518)
||....
T Consensus 160 Lr~~l~ 165 (228)
T PRK06704 160 LKTVSE 165 (228)
T ss_pred HHHHHH
Confidence 997543
No 121
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=99.54 E-value=1.1e-13 Score=140.51 Aligned_cols=155 Identities=15% Similarity=0.075 Sum_probs=113.7
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcccccc
Q 010092 278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357 (518)
Q Consensus 278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~ 357 (518)
+++..|.+.++.+|+++. ++..+.+|++||+|+.+++. .|+. ...|.+|++..+++.+.++++..+..+ .
T Consensus 1 ~l~~~~~~~l~~~a~r~l---g~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~-~-- 70 (281)
T TIGR02957 1 EEFEALRPLLFSLAYRML---GSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARR-E-- 70 (281)
T ss_pred ChHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcc-c--
Confidence 368899999999999998 77889999999999997775 4543 236999999999999998887211000 0
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcc
Q 010092 358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437 (518)
Q Consensus 358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ 437 (518)
.+ ... -+.. ...+ ...++
T Consensus 71 ------------------~~------------------------------~~~--~~~e-----------~~~~-~~~~~ 88 (281)
T TIGR02957 71 ------------------VY------------------------------VGP--WLPE-----------PLLT-TSADP 88 (281)
T ss_pred ------------------cc------------------------------CCC--CCCc-----------ccCC-CCCCh
Confidence 00 000 0000 0000 01123
Q ss_pred hhhhH-HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 438 ENQRQ-PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 438 ee~~~-~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
++... ...+...+..+|+.|||+||.||.|+| ..++|++|||+.||+|..+|++.++||+++||+..
T Consensus 89 ~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 89 AESVELAESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 33332 334556788999999999999999998 58999999999999999999999999999999743
No 122
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=99.53 E-value=1.6e-13 Score=140.38 Aligned_cols=160 Identities=13% Similarity=0.068 Sum_probs=118.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR 353 (518)
Q Consensus 274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR 353 (518)
..+..++..|.+.++.+|.++. ++..+++|++||.|+.+|++...+ . ..|.+|++...++.+.++++..+..+
T Consensus 5 ~~~~~l~~~~~~~L~~~a~r~l---gs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr 77 (290)
T PRK09635 5 DPVSAAWRAHRAYLVDLAFRMV---GDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRR 77 (290)
T ss_pred cHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccC
Confidence 5678999999999999999999 788899999999999999986543 1 25899999999999988887311100
Q ss_pred ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433 (518)
Q Consensus 354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~ 433 (518)
... ...+... .+ +... .
T Consensus 78 ~~~-------------------------------------------------------~~~~~~~---~~---~~~~--~ 94 (290)
T PRK09635 78 ERP-------------------------------------------------------QDIAAWH---DG---DASV--S 94 (290)
T ss_pred cCc-------------------------------------------------------ccccccC---cc---ccCC--C
Confidence 000 0000000 00 0000 1
Q ss_pred CCcchh-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 434 GVENEN-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 434 ~~~~ee-~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
..++++ .....+....+..+|..|||++|.||.|+| ..++|++|||+.||+|..+|+++++||+++||..
T Consensus 95 ~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 95 SVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 112222 233455667899999999999999999999 5799999999999999999999999999999974
No 123
>PRK09191 two-component response regulator; Provisional
Probab=99.43 E-value=1.6e-12 Score=128.33 Aligned_cols=136 Identities=8% Similarity=-0.040 Sum_probs=108.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccc
Q 010092 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV 354 (518)
Q Consensus 275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRl 354 (518)
++..|+..|.+.++.+|.++. ++..+.+|++||+|+.+|+....|++.. .|.+|++.++++.....
T Consensus 2 ~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~--------- 67 (261)
T PRK09191 2 SLSQRIAPHLPYLRRYARALT---GSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSA--------- 67 (261)
T ss_pred chHHHHHHHhHHHHHHHHHhc---CChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhccc---------
Confidence 578999999999999999998 7788999999999999999999998643 58888886654321000
Q ss_pred cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092 355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 434 (518)
Q Consensus 355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~ 434 (518)
.. .. ....
T Consensus 68 --------------------------------------------------------------~~--~~------~~~~-- 75 (261)
T PRK09191 68 --------------------------------------------------------------GA--ND------PEPG-- 75 (261)
T ss_pred --------------------------------------------------------------cc--cC------CCCC--
Confidence 00 00 0000
Q ss_pred CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.+.. ..+..+|+.||+++|.||.|+| .+++|++|||+.||+|.++|+....+|+++|+....
T Consensus 76 -~~~~--------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 76 -SPFE--------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred -CCch--------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 0110 1688999999999999999998 589999999999999999999999999999997654
No 124
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed
Probab=99.41 E-value=1.6e-11 Score=122.18 Aligned_cols=80 Identities=15% Similarity=0.207 Sum_probs=73.5
Q ss_pred HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP--RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI 342 (518)
Q Consensus 265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~--~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI 342 (518)
+..+..||..|++.|+..|.++|+++|.++. ++.. +.+|++|||++++|+++++|++++|..|.+|++.+|++.+
T Consensus 9 i~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~---~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~ 85 (237)
T PRK08311 9 LEKIKNGDEELREELIEEYKPFIAKVVSSVC---GRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL 85 (237)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---cccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence 4556789999999999999999999999998 4443 5899999999999999999999998889999999999999
Q ss_pred HHHHH
Q 010092 343 IRSMT 347 (518)
Q Consensus 343 ~raI~ 347 (518)
.++++
T Consensus 86 iDylR 90 (237)
T PRK08311 86 IDYFR 90 (237)
T ss_pred HHHHH
Confidence 99999
No 125
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=99.38 E-value=6.9e-12 Score=113.99 Aligned_cols=136 Identities=18% Similarity=0.220 Sum_probs=96.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHh-----cCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDR-----FEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350 (518)
Q Consensus 276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvek-----FDp~rG~kFSTYA~~wIRqaI~raI~~sr 350 (518)
++.++..|.++++.+|++|. . .+| +||.++.+|....+ |++. ..|.||++..+++.+.++++...
T Consensus 1 f~~~~~~y~~~l~~~~~~~~---~----~~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~ 70 (142)
T TIGR03209 1 FEEIYMNFKNTIDIFTRKYN---L----YYD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKN 70 (142)
T ss_pred ChHHHHHHHHHHHHHHHHhc---c----hhh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHh
Confidence 46799999999999999997 2 234 49999999999875 5432 46999999999999998887210
Q ss_pred CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092 351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT 430 (518)
Q Consensus 351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~ 430 (518)
.. .... . . .+ ++
T Consensus 71 ----------------~~--~~~~-~---~-------~~------------------------~~--------------- 82 (142)
T TIGR03209 71 ----------------RD--KKII-Y---N-------SE------------------------IT--------------- 82 (142)
T ss_pred ----------------hh--hhhh-h---h-------hh------------------------hh---------------
Confidence 00 0000 0 0 00 00
Q ss_pred cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 010092 431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 494 (518)
Q Consensus 431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVR 494 (518)
+.. ..+++.....+....|..+|+.||+.+|.||.|+| .+++|++|||+.||+|.++|+
T Consensus 83 ~~~-~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 83 DIK-LSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred ccc-cchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhc
Confidence 000 00111222334456688999999999999999998 589999999999999999997
No 126
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=99.31 E-value=6e-11 Score=113.48 Aligned_cols=175 Identities=19% Similarity=0.164 Sum_probs=115.9
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHH--HHHHHHHHHHHHHhcCCCCCCccchHHHHHHHH
Q 010092 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDL--CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH 340 (518)
Q Consensus 263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDL--IQEG~IGLirAvekFDp~rG~kFSTYA~~wIRq 340 (518)
+.|.++.+||..|.+.|+..|++-++.+|.++......+.+.+|. ++|.|+.++..-...+.+.-..|..|+...+++
T Consensus 6 ~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr 85 (185)
T PF07638_consen 6 ELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRR 85 (185)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHH
Confidence 347778999999999999999999999999877543344555554 667777776633322333333577777777777
Q ss_pred HHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC
Q 010092 341 AIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG 419 (518)
Q Consensus 341 aI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~ 419 (518)
.+.+.++ +....|-.. ....+||...
T Consensus 86 ~lid~~R~~~a~KRg~~----------------------------------------------------~~~~~l~~~~- 112 (185)
T PF07638_consen 86 KLIDHARRRQAQKRGGD----------------------------------------------------QVRVELDERA- 112 (185)
T ss_pred HHHHHHHHHHHHhcCCC----------------------------------------------------Ccccchhhhh-
Confidence 7777666 211110000 0001111110
Q ss_pred CchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 420 VTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 420 ~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+.+...++.. .++.+.+..+.. |+|++..+|.++| ..|+|.+|||+.||||..+|++....
T Consensus 113 ----------~~~~~~~~~~~---~~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~ 174 (185)
T PF07638_consen 113 ----------DSGDEPSPEEL---LELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRR 174 (185)
T ss_pred ----------ccccCCCHHHH---HHHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 00011122222 244555555555 9999999999988 58999999999999999999999999
Q ss_pred HHHHHhCcc
Q 010092 500 GLMKLKHPT 508 (518)
Q Consensus 500 ALkKLR~~~ 508 (518)
|..+|+..+
T Consensus 175 aR~~l~~~l 183 (185)
T PF07638_consen 175 ARAWLRREL 183 (185)
T ss_pred HHHHHHHHh
Confidence 999998654
No 127
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=99.19 E-value=4.1e-11 Score=90.65 Aligned_cols=50 Identities=46% Similarity=0.587 Sum_probs=45.8
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+|+.|||+|+.||.++| ++++|+.|||+.||+|.++|++++.+|+++||+
T Consensus 1 Al~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp HHCTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred ChhhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 58899999999999999 589999999999999999999999999999984
No 128
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=99.12 E-value=1.9e-10 Score=91.60 Aligned_cols=66 Identities=21% Similarity=0.312 Sum_probs=63.4
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (518)
Q Consensus 279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~ 347 (518)
|++.|.++|+.+|.+|. +++.+.+|++||++++||+++++||++.|..|.+|++..+++.+.+.++
T Consensus 1 L~~~~~~~l~~~~~~~~---~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r 66 (71)
T PF04542_consen 1 LYERYYPLLYRYARRYT---GDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLR 66 (71)
T ss_dssp HHHHTHHHHHHHHHTCT---TCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHh---CCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHH
Confidence 68999999999999998 7788999999999999999999999999988999999999999999998
No 129
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=98.93 E-value=2.3e-09 Score=88.17 Aligned_cols=75 Identities=37% Similarity=0.421 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCcchhh
Q 010092 366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ 440 (518)
Q Consensus 366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~ee~ 440 (518)
.+++|.++..+|.+++||.||.+|||+.|||++++|+.++.+...++||+.+...+++ .+.+.+.|+...+|++.
T Consensus 2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~ 77 (78)
T PF04539_consen 2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence 6789999999999999999999999999999999999999999999999998876644 56677777777777653
No 130
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=98.89 E-value=5.6e-09 Score=79.93 Aligned_cols=54 Identities=28% Similarity=0.329 Sum_probs=46.1
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 447 ~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
++.|..+|..|||+++.||.++| .+++|+.|||+.+|+|.++|++.+.+|+++|
T Consensus 1 r~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 1 REALQQALAQLPERQREIFLLRY----FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp HHHHHHHHHCS-HHHHHHHHHHH----TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 35789999999999999999999 5899999999999999999999999999987
No 131
>PRK06930 positive control sigma-like factor; Validated
Probab=98.47 E-value=4.7e-07 Score=86.01 Aligned_cols=66 Identities=20% Similarity=0.185 Sum_probs=58.7
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..........|..+|+.||++++.||.++| .+++|++|||+.||+|.++|++++.+|+++|+....
T Consensus 98 ~~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 98 SVISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 334455677899999999999999999988 489999999999999999999999999999997654
No 132
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=98.26 E-value=3.4e-06 Score=62.53 Aligned_cols=54 Identities=39% Similarity=0.467 Sum_probs=49.7
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
..+..++..|++.++.++.++| .+++|..+||+.+|+|..+|+++..++..+|+
T Consensus 2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3578889999999999999999 47899999999999999999999999998875
No 133
>PRK00118 putative DNA-binding protein; Validated
Probab=98.19 E-value=5e-06 Score=72.77 Aligned_cols=59 Identities=25% Similarity=0.238 Sum_probs=52.1
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
..++-....||++++.|+.++| .+++|..|||+.+|+|+.+|++++.+|+++||+....
T Consensus 9 ~l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~ 67 (104)
T PRK00118 9 LLFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK 67 (104)
T ss_pred HHHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566789999999999999 5899999999999999999999999999999986544
No 134
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=98.15 E-value=4.3e-06 Score=76.62 Aligned_cols=55 Identities=18% Similarity=0.170 Sum_probs=48.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 515 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~ 515 (518)
-||++|+.||.+++ +++|++|||+.||+|+++|++++++|+++|+.....-.|..
T Consensus 6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~ 60 (137)
T TIGR00721 6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVK 60 (137)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHH
Confidence 59999999999976 79999999999999999999999999999997655444433
No 135
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=98.04 E-value=7.9e-06 Score=75.26 Aligned_cols=50 Identities=26% Similarity=0.213 Sum_probs=46.1
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..|+|+|++||.+++ +++|++|||+.||+|+.+|++++++|+++||+...
T Consensus 5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 469999999999976 79999999999999999999999999999997654
No 136
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=97.97 E-value=3.2e-05 Score=67.22 Aligned_cols=55 Identities=29% Similarity=0.330 Sum_probs=43.7
Q ss_pred HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 449 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 449 ~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.|.+.... |+++|+.++.++| .+++|+.|||+.+|||+.+|...+.||.++|...
T Consensus 9 ~L~d~Yg~LLT~kQ~~~l~lyy----~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~y 64 (101)
T PF04297_consen 9 LLFDFYGELLTEKQREILELYY----EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEY 64 (101)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHC----TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHH----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44555544 8999999999999 6899999999999999999999999999999754
No 137
>PRK04217 hypothetical protein; Provisional
Probab=97.93 E-value=1.4e-05 Score=70.63 Aligned_cols=55 Identities=15% Similarity=-0.040 Sum_probs=49.4
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L 513 (518)
..|++.|++||.++| .+++|++|||+.||||+.+|++++.+|.++|+.......+
T Consensus 41 ~~Lt~eereai~l~~----~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~ 95 (110)
T PRK04217 41 IFMTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE 95 (110)
T ss_pred ccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 479999999999998 5899999999999999999999999999999987665443
No 138
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.87 E-value=4e-05 Score=57.74 Aligned_cols=50 Identities=36% Similarity=0.358 Sum_probs=44.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..|++.|+.|+.+.+ .++|..|||+.||+|+.+|+++..+++.+|.-...
T Consensus 2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~ 51 (58)
T smart00421 2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSR 51 (58)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence 468999999998755 68999999999999999999999999999986554
No 139
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=97.81 E-value=6.3e-05 Score=68.70 Aligned_cols=61 Identities=18% Similarity=0.194 Sum_probs=53.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.....|..+|+.|++.++.||.++|+ . ...+|..+||..||+|+.+|+++..+|+.+|...
T Consensus 71 ~~~~~I~~~l~~Ld~~er~II~~rY~-~-~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 71 RNRDAIENCLNEADEQTRVIIQELYM-K-KRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc-c-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999994 1 1236999999999999999999999999999864
No 140
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=97.72 E-value=1.3e-05 Score=57.22 Aligned_cols=33 Identities=21% Similarity=0.245 Sum_probs=29.1
Q ss_pred cChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010092 200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK 232 (518)
Q Consensus 200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~ 232 (518)
+|+++.||++|+.+|+||++||..|++.|+.+.
T Consensus 1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~ 33 (37)
T PF00140_consen 1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGD 33 (37)
T ss_dssp HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhH
Confidence 478999999999999999999999999997654
No 141
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=97.71 E-value=0.00014 Score=54.86 Aligned_cols=49 Identities=35% Similarity=0.366 Sum_probs=43.9
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
|+++|+.|+.+.+ .++|.+|||+.||+|..+|+++..+++++|......
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~~ 49 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT 49 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHH
Confidence 6899999998865 689999999999999999999999999999986543
No 142
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=97.68 E-value=0.00012 Score=56.88 Aligned_cols=52 Identities=31% Similarity=0.319 Sum_probs=44.6
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
+.|+++|.+||.+.. .|+|.+|||..+|+|..+|+.+..++++||.-..+.+
T Consensus 2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~ 53 (58)
T PF00196_consen 2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAE 53 (58)
T ss_dssp GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHH
T ss_pred CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHH
Confidence 479999999999887 7999999999999999999999999999998766544
No 143
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=97.66 E-value=0.00018 Score=62.41 Aligned_cols=56 Identities=32% Similarity=0.481 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 445 LLRLALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 445 ~l~~~L~~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
..+..|..+++.| ++.+|.||.++| ...++..+||+.||+|+.++..+..+|++.|
T Consensus 43 ~~k~ei~~~I~~l~d~~~r~iL~~~Y----i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 43 KEKLEIRRAINKLEDPDERLILRMRY----INKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred HHHHHHHHHHHHccChhHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4456688889898 489999999999 4789999999999999999999999999876
No 144
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=97.57 E-value=0.00027 Score=54.51 Aligned_cols=48 Identities=27% Similarity=0.373 Sum_probs=41.3
Q ss_pred CCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 457 L~~rEr~VL~lry--GL~~~-e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
|+++|+++|..-| |..+. ..-|+.|||+.||||.+++..++.+|.+||
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl 51 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL 51 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 7899999998755 44343 368999999999999999999999999987
No 145
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.57 E-value=9.7e-05 Score=63.36 Aligned_cols=51 Identities=20% Similarity=0.248 Sum_probs=43.6
Q ss_pred HHHHHHHh-cCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 448 LALDDVLD-SLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 448 ~~L~~~L~-~L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+.+..+|. -|+|+|+.+|.+||||.+ ..++|+.|||+.+|||+.+|.+..+
T Consensus 23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 34666674 499999999999999987 6789999999999999999986643
No 146
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.48 E-value=0.00023 Score=58.41 Aligned_cols=48 Identities=21% Similarity=0.192 Sum_probs=41.5
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+.+-|+.||++.+.++.|.+- .+++|+.|||+.||+|..+|++++++
T Consensus 8 ~~~~~l~~l~~~~r~af~L~R~---~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 8 KLAERLTWVDSLAEAAAALARE---EAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hHHHHHhcCCHHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4566788999999999999531 48999999999999999999999874
No 147
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=97.30 E-value=0.00058 Score=64.96 Aligned_cols=51 Identities=20% Similarity=0.164 Sum_probs=47.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
.|+++|++||.+.- +|+|.+|||+.|++|..||+....++++||.-..+.+
T Consensus 133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~SRaE 183 (198)
T PRK15201 133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQ 183 (198)
T ss_pred CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 59999999999887 8999999999999999999999999999998766654
No 148
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=97.30 E-value=0.00043 Score=67.46 Aligned_cols=50 Identities=24% Similarity=0.268 Sum_probs=46.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
.|+++|++||.+.- +|+|.+|||+.||+|..||+.+..+.++||.-..+.
T Consensus 137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~nr~ 186 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQ 186 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCCcHH
Confidence 59999999999887 799999999999999999999999999999865553
No 149
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=97.24 E-value=0.00052 Score=66.20 Aligned_cols=52 Identities=31% Similarity=0.328 Sum_probs=46.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
..|++||++|+.+.- +|+|.+|||+.|++|..||+.+..+.++||--..+.+
T Consensus 149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~ 200 (216)
T PRK10840 149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIA 200 (216)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 359999999999887 7999999999999999999999999999997654443
No 150
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=97.23 E-value=0.00052 Score=67.13 Aligned_cols=52 Identities=21% Similarity=0.279 Sum_probs=46.9
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
..|++||++||.+.- +|+|.+|||+.|++|..||+.+..+.++||--..+.+
T Consensus 133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~n~~e 184 (207)
T PRK11475 133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAG 184 (207)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 469999999999887 7999999999999999999999999999997655443
No 151
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=97.23 E-value=0.00066 Score=67.36 Aligned_cols=54 Identities=26% Similarity=0.187 Sum_probs=48.3
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
...||++|++||.+.. +++|..|||+.||||..+|+.++.+|++||.-..+.+.
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~a 222 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA 222 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 3479999999999976 79999999999999999999999999999997766543
No 152
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=97.23 E-value=0.00063 Score=68.48 Aligned_cols=54 Identities=24% Similarity=0.202 Sum_probs=49.0
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
+..||++|++||.+.. +++|.+|||+.||||..||+.+..++++||.-..+.+.
T Consensus 188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~qA 241 (247)
T TIGR03020 188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA 241 (247)
T ss_pred ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 4579999999999976 79999999999999999999999999999998776654
No 153
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=97.21 E-value=0.00077 Score=66.22 Aligned_cols=56 Identities=14% Similarity=-0.043 Sum_probs=50.4
Q ss_pred HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 451 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 451 ~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
.++...|+|+|++||.+.- +|+|.+|||+.|++|..||+.+..+.++||--..+.+
T Consensus 138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~e 193 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDE 193 (217)
T ss_pred hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 4566789999999999887 7999999999999999999999999999998766654
No 154
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=97.18 E-value=0.00076 Score=66.37 Aligned_cols=52 Identities=23% Similarity=0.210 Sum_probs=47.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
..|+++|++|+.+.+ +|+|.+|||+.|++|..||+.+..++++||.-..+.+
T Consensus 154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 469999999999998 6999999999999999999999999999998766654
No 155
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=97.08 E-value=0.002 Score=62.01 Aligned_cols=67 Identities=24% Similarity=0.255 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ 515 (518)
Q Consensus 444 ~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~ 515 (518)
......+...+.+|+||||+|+...- .++..++||..||||..||..+-...+.||+.....+-++-
T Consensus 130 ~~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~ 196 (202)
T COG4566 130 ADRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRM 196 (202)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHH
Confidence 34556788899999999999999876 78999999999999999999999999999998766555443
No 156
>PRK13870 transcriptional regulator TraR; Provisional
Probab=97.06 E-value=0.001 Score=66.34 Aligned_cols=52 Identities=21% Similarity=0.240 Sum_probs=47.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
.|++||++||.+-= +|+|..|||.+||||..||..+++.|.+||--..+.+.
T Consensus 173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~qA 224 (234)
T PRK13870 173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL 224 (234)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence 49999999999886 89999999999999999999999999999987665543
No 157
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=97.05 E-value=0.0025 Score=49.62 Aligned_cols=54 Identities=31% Similarity=0.359 Sum_probs=47.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L 513 (518)
..|+++|.+|+.+.- .++|..|||..+|+|..+|+.+..++.+||.-..+.+.+
T Consensus 3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~ 56 (65)
T COG2771 3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELV 56 (65)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Confidence 369999999998876 579999999999999999999999999999877665443
No 158
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.04 E-value=0.00085 Score=49.60 Aligned_cols=41 Identities=27% Similarity=0.328 Sum_probs=24.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..|++.|+..|...+ ..++|..+||+.||+|++||+..+.|
T Consensus 3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999999888 68899999999999999999998876
No 159
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=97.00 E-value=0.0015 Score=64.04 Aligned_cols=53 Identities=32% Similarity=0.339 Sum_probs=47.6
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
..|++||++|+++.- +|+|.+|||+.|++|..||+.+..+.++||.-..+.+-
T Consensus 147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea 199 (211)
T COG2197 147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEA 199 (211)
T ss_pred CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCCHHHH
Confidence 469999999999876 79999999999999999999999999999987665543
No 160
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=96.98 E-value=0.0016 Score=65.13 Aligned_cols=52 Identities=23% Similarity=0.288 Sum_probs=47.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
.|+++|++||.+-. +|+|..|||.+||||..||+.++..+++||--..+.+.
T Consensus 179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~ 230 (240)
T PRK10188 179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI 230 (240)
T ss_pred CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 59999999999987 79999999999999999999999999999987665543
No 161
>PRK09483 response regulator; Provisional
Probab=96.83 E-value=0.0021 Score=60.91 Aligned_cols=51 Identities=24% Similarity=0.255 Sum_probs=45.2
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
..|+++|++||.+.. .++|.+|||+.|++|..||+.+..+.++||--..+.
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~ 197 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDV 197 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 469999999998765 789999999999999999999999999999654443
No 162
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=96.79 E-value=0.0028 Score=62.17 Aligned_cols=51 Identities=24% Similarity=0.310 Sum_probs=43.8
Q ss_pred cCCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lry--GL~~~-e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+++|++||..-| |..+. ...+++|||+.||||.+++.+++.+|.+||=.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 69999999999855 54443 35899999999999999999999999999853
No 163
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.74 E-value=0.005 Score=53.30 Aligned_cols=47 Identities=23% Similarity=0.285 Sum_probs=42.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
-|+.+|+..+.++| ..++|+.|||+.++||+++|...++|.-+.|-.
T Consensus 17 LLT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 17 LLTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 38999999999999 589999999999999999999999999777654
No 164
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=96.73 E-value=0.0035 Score=70.92 Aligned_cols=38 Identities=16% Similarity=0.156 Sum_probs=34.2
Q ss_pred hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010092 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK 232 (518)
Q Consensus 195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~ 232 (518)
+.+.++|+|+|||++||.+||||.|+|+.+++.|+.+.
T Consensus 98 ~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~ 135 (619)
T PRK05658 98 EIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE 135 (619)
T ss_pred ccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence 34568999999999999999999999999999997654
No 165
>PRK01381 Trp operon repressor; Provisional
Probab=96.69 E-value=0.0014 Score=56.69 Aligned_cols=50 Identities=18% Similarity=0.224 Sum_probs=41.7
Q ss_pred HHHHHHHHHhc-CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHH
Q 010092 446 LRLALDDVLDS-LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRK 495 (518)
Q Consensus 446 l~~~L~~~L~~-L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRq 495 (518)
....+..+|.. |+|.|+..|..||++.. ..++|+.|||+.+|||..+|.+
T Consensus 21 ~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR 74 (99)
T PRK01381 21 EEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR 74 (99)
T ss_pred cHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence 34456666766 89999999999999976 4579999999999999988873
No 166
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.69 E-value=0.0033 Score=55.25 Aligned_cols=49 Identities=18% Similarity=0.081 Sum_probs=44.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
.|+..|-+.|+|.+ ++++|.+|-|+.||||+.|+..++..|.+|+-..+
T Consensus 41 ~L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 41 VLTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred EeeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 58889999999988 58999999999999999999999999999997644
No 167
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=96.63 E-value=0.0073 Score=55.51 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=51.1
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
.+...+..|+++|+.||.+.+ .+++.++||+.+|+|..+|+.+..++++||+...+.+-
T Consensus 134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~~ 192 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSEL 192 (202)
T ss_pred HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccccHHHH
Confidence 455667789999999999755 57899999999999999999999999999987766553
No 168
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=96.53 E-value=0.0069 Score=55.96 Aligned_cols=51 Identities=25% Similarity=0.285 Sum_probs=45.3
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
..|+++|++||.+.- +++|.+|||+.|++|..||+.+..++++||.-..+.
T Consensus 148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~ 198 (211)
T PRK15369 148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVA 198 (211)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHH
Confidence 359999999999843 789999999999999999999999999999865543
No 169
>PRK10651 transcriptional regulator NarL; Provisional
Probab=96.50 E-value=0.0061 Score=57.03 Aligned_cols=52 Identities=27% Similarity=0.337 Sum_probs=46.5
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
..|+++|++|+.+.. ++++.++||+.+++|..||+.+..+.++||.-..+.+
T Consensus 154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~~ 205 (216)
T PRK10651 154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE 205 (216)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 359999999999866 7899999999999999999999999999998665544
No 170
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=96.44 E-value=0.016 Score=52.51 Aligned_cols=60 Identities=10% Similarity=0.146 Sum_probs=50.7
Q ss_pred HHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 446 LRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 446 l~~~L~~~L-~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
....+..++ +.|++.+|.||.++|. + .++++..+|+..||+|+.+...+.++|+.++-..
T Consensus 68 ~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~ 128 (132)
T TIGR01637 68 EARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL 128 (132)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence 345677777 8999999999999994 1 1278999999999999999999999999988644
No 171
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.38 E-value=0.0023 Score=57.44 Aligned_cols=50 Identities=24% Similarity=0.199 Sum_probs=45.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~ 510 (518)
-|+++|-.||.||- .|+|.+|||++||-|+..|+-|+.+|+.++.+..+.
T Consensus 8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT 57 (143)
T COG1356 8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT 57 (143)
T ss_pred eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence 38999999999997 899999999999999999999999999999876543
No 172
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=96.12 E-value=0.02 Score=45.97 Aligned_cols=60 Identities=25% Similarity=0.230 Sum_probs=48.9
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhc-c--CCCCCHHHHHHHHHHHHHHHHHhcC
Q 010092 264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD-F--ANGPRFQDLCQAGVKGLITAIDRFE 323 (518)
Q Consensus 264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~-~--~~g~~~eDLIQEG~IGLirAvekFD 323 (518)
.|.++.+||..|.++++.+|-|++.+.+.+-..+ . ..+.-=+||-|+-...|++++-+|+
T Consensus 3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~ 65 (65)
T PF12645_consen 3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE 65 (65)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence 4677899999999999999999999988862211 0 1244459999999999999999996
No 173
>PRK10403 transcriptional regulator NarP; Provisional
Probab=96.04 E-value=0.015 Score=54.15 Aligned_cols=54 Identities=30% Similarity=0.241 Sum_probs=47.4
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L 513 (518)
..|+++|.+|+.+.. +++|.++||+.+|+|..||+.+..+.++||.-..+.+-.
T Consensus 152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~~~ 205 (215)
T PRK10403 152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAAT 205 (215)
T ss_pred ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 359999999998776 689999999999999999999999999999776665543
No 174
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=95.96 E-value=0.021 Score=53.11 Aligned_cols=57 Identities=26% Similarity=0.310 Sum_probs=49.1
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQH 516 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y 516 (518)
..|+++|.+|+.+.. +++|.++||+.|++|..+|+.+..+.++||.-..+.+-...|
T Consensus 136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~~~ 192 (196)
T PRK10360 136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRM 192 (196)
T ss_pred cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 369999999999876 579999999999999999999999999999877666544433
No 175
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.93 E-value=0.014 Score=56.59 Aligned_cols=51 Identities=10% Similarity=0.068 Sum_probs=45.6
Q ss_pred HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 452 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 452 ~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.+--.|+++|.+|+.+-- .|+|.+|||+.|++|..+|+...++.+.||.-.
T Consensus 160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence 334579999999998876 799999999999999999999999999999754
No 176
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.53 E-value=0.026 Score=48.47 Aligned_cols=48 Identities=21% Similarity=0.067 Sum_probs=43.4
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
.|+..|-+.|+|.. ++++|.+|-|..||||+.|+-+.++.|.+|.-..
T Consensus 33 ~lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~a 80 (99)
T COG1342 33 ILTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKVADA 80 (99)
T ss_pred eecHHHHHHHHHHh----HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence 47778889999988 6899999999999999999999999999998654
No 177
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=95.40 E-value=0.058 Score=49.20 Aligned_cols=58 Identities=26% Similarity=0.334 Sum_probs=48.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
....|..+++.|.+.++.||.+||+ +..++|..+||..|++|..+++.+...-...++
T Consensus 71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 4567888899999999999999996 234699999999999999999988776555443
No 178
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=95.35 E-value=0.039 Score=51.53 Aligned_cols=49 Identities=24% Similarity=0.209 Sum_probs=43.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
.|+++|..|+.+.. +++|.+|||+.|++|..||+.+..++++||.-..+
T Consensus 149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (210)
T PRK09935 149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSI 197 (210)
T ss_pred cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 48999999998654 67999999999999999999999999999975544
No 179
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=95.20 E-value=0.042 Score=46.84 Aligned_cols=39 Identities=15% Similarity=0.193 Sum_probs=32.2
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+.|++| ..|+.+.- .++|..+||+.+|+|+.||.++. ++
T Consensus 35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~-R~ 73 (88)
T TIGR02531 35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK-RC 73 (88)
T ss_pred HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH-Hh
Confidence 458899 78877765 57999999999999999999944 44
No 180
>PRK13558 bacterio-opsin activator; Provisional
Probab=95.19 E-value=0.035 Score=62.79 Aligned_cols=52 Identities=17% Similarity=0.153 Sum_probs=43.4
Q ss_pred HhcCCHHHHHHHhHHhcCC--CC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 454 LDSLKPKESLVIRQRFGLD--GK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~--~~-e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
...|+++|+++|..-|-.+ +. .+-|++|||+.||||++++.+++.+|.+||=
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~ 659 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLV 659 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3579999999999977321 11 2359999999999999999999999999984
No 181
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=95.18 E-value=0.047 Score=51.03 Aligned_cols=50 Identities=26% Similarity=0.285 Sum_probs=44.7
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~ 509 (518)
..|+++|.+|+.+.. .+.|.++||+.+++|..||+.+..+..+||.-..+
T Consensus 142 ~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~ 191 (204)
T PRK09958 142 DSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSL 191 (204)
T ss_pred ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence 469999999998877 67899999999999999999999999999965443
No 182
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.14 E-value=0.046 Score=41.82 Aligned_cols=48 Identities=17% Similarity=0.168 Sum_probs=42.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+|+..++.++.+.|- ..+.|++.+|..+|||+++|+++.+..+.-|-.
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 588899999888774 678999999999999999999999998877754
No 183
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=95.13 E-value=0.046 Score=44.57 Aligned_cols=39 Identities=36% Similarity=0.674 Sum_probs=30.8
Q ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 231 MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 231 ~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
+..+.++..+|+..+||.|+..|+|..+|++.+.+..++
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence 345677888999999999999999999999998887655
No 184
>PRK04841 transcriptional regulator MalT; Provisional
Probab=95.09 E-value=0.042 Score=64.14 Aligned_cols=53 Identities=21% Similarity=0.277 Sum_probs=47.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
..|+++|.+|+.+.. +++|.+|||..|+||..||+.++++...||.-..+.+.
T Consensus 837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~~r~~~ 889 (903)
T PRK04841 837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA 889 (903)
T ss_pred CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence 349999999999977 89999999999999999999999999999987666543
No 185
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.98 E-value=0.022 Score=42.50 Aligned_cols=33 Identities=27% Similarity=0.256 Sum_probs=23.2
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.||.+.. +++|..+||+.||||+.+|+++.++-
T Consensus 9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 4555555 58999999999999999999997764
No 186
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=94.98 E-value=0.59 Score=49.05 Aligned_cols=57 Identities=19% Similarity=0.339 Sum_probs=48.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++...--+--.|++.+|.-|.+|. ..++|..|||..|=|+..++-|.+.||.++++.
T Consensus 110 LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 110 LRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred HHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 333333333459999999999998 679999999999999999999999999999996
No 187
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=94.73 E-value=0.28 Score=52.15 Aligned_cols=129 Identities=22% Similarity=0.286 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~ 312 (518)
.+......|...+|++|+..|+|..+|++.+.+..++.... -.+++-... +.+ +|
T Consensus 217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~------------~~~SLd~~~----~~~---~~------ 271 (367)
T PRK09210 217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ------------EPVSLETPI----GEE---DD------ 271 (367)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc------------CCCCcCCCC----CCC---Cc------
Confidence 44566677888999999999999999999988876542210 001110000 000 01
Q ss_pred HHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHH--hCCCCCHHHH
Q 010092 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFE--LKRVPTDEEI 390 (518)
Q Consensus 313 IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~e--lgR~PT~eEL 390 (518)
..|...+. |+.............++..+..++.. +|. -.+..-.+..- .|.+-|.+||
T Consensus 272 ~~l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~-----L~~-------------rEr~Vl~lrygl~~~~~~tl~EI 331 (367)
T PRK09210 272 SHLGDFIE--DQDATSPADHAAYELLKEQLEDVLDT-----LTD-------------REENVLRLRFGLDDGRTRTLEEV 331 (367)
T ss_pred chhhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh-----CCH-------------HHHHHHHHHhccCCCCCccHHHH
Confidence 01111111 11112223344555666677666651 222 11111122221 2377899999
Q ss_pred HHHhCCCHHHHHHHHH
Q 010092 391 IQGVNISPERYREVMK 406 (518)
Q Consensus 391 A~~lgis~e~v~~~l~ 406 (518)
|+.+|+|.++|+.+..
T Consensus 332 a~~lgvs~erVrQi~~ 347 (367)
T PRK09210 332 GKVFGVTRERIRQIEA 347 (367)
T ss_pred HHHHCCCHHHHHHHHH
Confidence 9999999999998854
No 188
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=94.44 E-value=0.066 Score=39.56 Aligned_cols=33 Identities=18% Similarity=0.118 Sum_probs=24.1
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 461 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 461 Er~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
...|+.|+- +++|..+||+.+|||+.||.+++.
T Consensus 11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence 355666665 679999999999999999998763
No 189
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=94.40 E-value=0.11 Score=38.53 Aligned_cols=41 Identities=24% Similarity=0.167 Sum_probs=30.1
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
|++.++.||..-+= .++.|..|||+.+|+|..+|++++++-
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L 41 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL 41 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56788888876552 456999999999999999999877654
No 190
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=93.98 E-value=0.058 Score=37.38 Aligned_cols=26 Identities=38% Similarity=0.431 Sum_probs=18.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
++|.+|||+.+|+|+++|++ ++++|+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR----~l~~l~ 27 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSR----ILKKLE 27 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHH----HHHHHH
Confidence 47899999999999999995 455554
No 191
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=93.88 E-value=0.7 Score=48.47 Aligned_cols=36 Identities=33% Similarity=0.593 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+......|...+|++|+..|+|..+|++.+.+..+
T Consensus 174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~ 209 (324)
T PRK07921 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADL 209 (324)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 445667778889999999999999999998777654
No 192
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=93.76 E-value=0.084 Score=55.13 Aligned_cols=36 Identities=22% Similarity=0.204 Sum_probs=32.2
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
.|-.||| .+++|.+|||++||+||.+|.+++.+|.+
T Consensus 20 ~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 20 RIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4566788 68999999999999999999999999965
No 193
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=93.76 E-value=0.73 Score=51.20 Aligned_cols=36 Identities=31% Similarity=0.556 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+...+.+|...+|++|+..|+|..+|++.+.+..+
T Consensus 359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 445667788889999999999999999998877654
No 194
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=93.68 E-value=0.13 Score=33.91 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=27.6
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 496 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqi 496 (518)
+++.++..+...| ..+.|..+||+.+|+|+.+|.++
T Consensus 6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence 4555565555555 35679999999999999999875
No 195
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=93.32 E-value=0.11 Score=41.64 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=28.6
Q ss_pred HhcCCHHHHHHHhH--HhcCCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQ--RFGLDGKGDRTLGEIAGNLNIS-REMVRKHEVK 499 (518)
Q Consensus 454 L~~L~~rEr~VL~l--ryGL~~~e~~Tl~EIA~~LgIS-rerVRqie~r 499 (518)
|..|+++|++||.. .|--..+-+-|+.|||+.||++ .++|.+++..
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 45799999999876 2222223467999999999997 9999877643
No 196
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=93.25 E-value=0.94 Score=44.92 Aligned_cols=36 Identities=44% Similarity=0.712 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+......+...+|++|+.+|+|..+|++.+.+..+
T Consensus 88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~ 123 (238)
T TIGR02393 88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI 123 (238)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 344566778889999999999999999998877654
No 197
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=92.41 E-value=0.94 Score=49.11 Aligned_cols=39 Identities=18% Similarity=0.162 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVM 405 (518)
Q Consensus 367 ~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l 405 (518)
...+.+....|..++|++||.+|.|..+|+++.+++..+
T Consensus 110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l 148 (415)
T PRK07598 110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL 148 (415)
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence 345566778899999999999999988887766665544
No 198
>PF13518 HTH_28: Helix-turn-helix domain
Probab=92.39 E-value=0.28 Score=36.50 Aligned_cols=27 Identities=26% Similarity=0.254 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
++.|+.+||..+|||+.+|+++..+-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456999999999999999999887653
No 199
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=92.31 E-value=0.32 Score=43.33 Aligned_cols=50 Identities=28% Similarity=0.256 Sum_probs=42.9
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.+..|++.+..-|..+. ...=+++|+++.||||..|||..+.+.+.+|-.
T Consensus 30 ~~~~L~~E~~~Fi~~Fi----~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 30 WFARLSPEQLEFIKLFI----KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hhhcCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 35689998888887665 234589999999999999999999999999986
No 200
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=92.09 E-value=0.7 Score=41.75 Aligned_cols=50 Identities=18% Similarity=0.110 Sum_probs=44.9
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
|..-.|.+-.+|.++| ..++|...||..+++|...||+.+.+|-.-+...
T Consensus 60 L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~ 109 (125)
T PF06530_consen 60 LKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGC 109 (125)
T ss_pred HHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhh
Confidence 4457999999999999 4799999999999999999999999998888765
No 201
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=92.06 E-value=0.4 Score=35.12 Aligned_cols=39 Identities=23% Similarity=0.368 Sum_probs=26.7
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
++-.+.||..--. ....|+.+||+.+|+|..+|.+...+
T Consensus 2 D~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 2 DELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 4456666665442 35799999999999999999977654
No 202
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=92.06 E-value=2.4 Score=42.90 Aligned_cols=38 Identities=32% Similarity=0.561 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 232 ~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
..+..+.+.|+.++||+||+.|+|...|++.+++...+
T Consensus 110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~ 147 (247)
T COG1191 110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEAL 147 (247)
T ss_pred HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHH
Confidence 44567788899999999999999999999987765544
No 203
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=92.05 E-value=0.3 Score=38.37 Aligned_cols=26 Identities=23% Similarity=0.270 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.+++..|||+.||+++.+|.+...+-
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 79999999999999999999998775
No 204
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=92.04 E-value=0.25 Score=39.20 Aligned_cols=26 Identities=31% Similarity=0.519 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
...+++.+||+.||||..+||....+
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence 45899999999999999999988764
No 205
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.81 E-value=0.17 Score=38.88 Aligned_cols=40 Identities=28% Similarity=0.322 Sum_probs=27.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|+..|+.=|.-+| ..+.+..+||..|||+.+||+.|...
T Consensus 6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 46666666555566 36779999999999999999999875
No 206
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.58 E-value=0.56 Score=35.54 Aligned_cols=46 Identities=24% Similarity=0.362 Sum_probs=32.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 456 SLKPKESLVIRQRFGLDGKGD---RTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~---~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.|++.++.|+..-.-+.+..+ .|.+.||+.+|+|+.+|++ +++.|.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~----~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQR----AIKELE 50 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHH
Confidence 588888888766443322222 3899999999999999984 555554
No 207
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=91.50 E-value=0.36 Score=47.33 Aligned_cols=47 Identities=23% Similarity=0.164 Sum_probs=36.8
Q ss_pred cCCHHHHHHHhHHh-cCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRF-GLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 456 ~L~~rEr~VL~lry-GL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
.|+++|.+++.... +. ..+++|.+|||+.||+|..||+.+..++...
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 48899977764433 11 1378999999999999999999999988554
No 208
>smart00351 PAX Paired Box domain.
Probab=90.91 E-value=0.54 Score=42.37 Aligned_cols=42 Identities=19% Similarity=0.059 Sum_probs=32.7
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
|+..+|.-|...| .++.|..+||+.||||+.+|.++.++...
T Consensus 18 ~s~~~R~riv~~~----~~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 18 LPDEERQRIVELA----QNGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4555555555555 36789999999999999999999998753
No 209
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=90.89 E-value=2 Score=45.95 Aligned_cols=36 Identities=25% Similarity=0.501 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHH
Q 010092 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKK 267 (518)
Q Consensus 232 ~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~ 267 (518)
..+......|...+|+.|+..|+|..+|++.+.+..
T Consensus 223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~ 258 (373)
T PRK07406 223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF 258 (373)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 344556677888999999999999999999877754
No 210
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=90.36 E-value=0.43 Score=36.15 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=27.6
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
|+..||.+-+ ...++.|.+|||+.||||+.+|++.+..-
T Consensus 1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L 39 (55)
T PF08279_consen 1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4556665542 22345999999999999999999776654
No 211
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=90.20 E-value=0.59 Score=35.97 Aligned_cols=44 Identities=25% Similarity=0.246 Sum_probs=32.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.|++.|..||..-+.-++ .+.|..|||+.+++++.+|.++.++-
T Consensus 2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~L 45 (62)
T PF12802_consen 2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKRL 45 (62)
T ss_dssp TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 378888888887664221 23899999999999999999776654
No 212
>PHA00675 hypothetical protein
Probab=89.85 E-value=0.65 Score=38.49 Aligned_cols=40 Identities=18% Similarity=0.105 Sum_probs=30.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|++-+-+.|+..+- ..+.|+.+||..||||+++|.+|.+
T Consensus 22 KLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 566666665555441 2577999999999999999999875
No 213
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=89.84 E-value=0.65 Score=34.41 Aligned_cols=37 Identities=27% Similarity=0.391 Sum_probs=27.9
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
|.-..||.+-. ..+++..||++.+|+|+++|++++..
T Consensus 2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~ 38 (47)
T PF01022_consen 2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK 38 (47)
T ss_dssp HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence 44455665554 36899999999999999999988754
No 214
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=89.66 E-value=1.3 Score=44.70 Aligned_cols=36 Identities=33% Similarity=0.589 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+..+..+|...+|++|+..|+|..+|++.+.+..+
T Consensus 114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~ 149 (256)
T PRK07408 114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI 149 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 445667788889999999999999999998877554
No 215
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=89.63 E-value=0.49 Score=49.61 Aligned_cols=35 Identities=29% Similarity=0.203 Sum_probs=30.6
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+-.+|| .+++|..|||++||||+.+|++++.+|.+
T Consensus 18 ~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 18 AAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 345677 68999999999999999999999999864
No 216
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=89.48 E-value=0.72 Score=39.10 Aligned_cols=44 Identities=30% Similarity=0.240 Sum_probs=34.0
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL--NISREMVRKHEVKG 500 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L--gISrerVRqie~rA 500 (518)
++.||+..+++..+|.- ..+.|+.|+|+.| .||++.|..+..+-
T Consensus 35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl 80 (85)
T PF02650_consen 35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL 80 (85)
T ss_dssp GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence 47899999999999874 5789999999999 99999998877664
No 217
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=89.48 E-value=0.48 Score=54.96 Aligned_cols=51 Identities=27% Similarity=0.159 Sum_probs=46.5
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~ 512 (518)
||.||.+|+.+.| .|+|.+|||+++.||-.||+.+...--.||.-..+.+.
T Consensus 832 Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqA 882 (894)
T COG2909 832 LSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQA 882 (894)
T ss_pred ccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHH
Confidence 8999999999999 79999999999999999999999999999976655443
No 218
>PHA02591 hypothetical protein; Provisional
Probab=89.20 E-value=0.46 Score=39.46 Aligned_cols=24 Identities=29% Similarity=0.209 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|+|.++||+.||+|.++|+++..
T Consensus 58 qGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 58 KGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHh
Confidence 589999999999999999999875
No 219
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=88.46 E-value=15 Score=38.22 Aligned_cols=176 Identities=14% Similarity=0.015 Sum_probs=89.8
Q ss_pred HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccc
Q 010092 281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLES 360 (518)
Q Consensus 281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e 360 (518)
...+..+-.++... .+.+-+.|...-+++.+.....-+|.....++.-.|.-++.
T Consensus 123 ~~a~~~I~~~~~~L--------~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR----------------- 177 (310)
T PRK00423 123 AFALSELDRIASQL--------GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR----------------- 177 (310)
T ss_pred HHHHHHHHHHHHHc--------CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH-----------------
Confidence 33445555555544 34466777777788877666767787665555434333332
Q ss_pred hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhh
Q 010092 361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 440 (518)
Q Consensus 361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~ 440 (518)
..|-+-|..||++.++++..++....+.-...+.++.+.. +..+++..+.+.-..+ .+.
T Consensus 178 -------------------~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~-~p~~~i~r~~~~L~L~-~~v 236 (310)
T PRK00423 178 -------------------RCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT-DPIDYVPRFASELGLS-GEV 236 (310)
T ss_pred -------------------HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC-CHHHHHHHHHHHcCCC-HHH
Confidence 1234456777888888888777655443322222322221 1223332222211111 111
Q ss_pred hHHHHHHHHHHHHHh-cC----CHHH--HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 441 RQPALLRLALDDVLD-SL----KPKE--SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 441 ~~~~~l~~~L~~~L~-~L----~~rE--r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.. .-...+..+.+ .| +|.- ..+|.+-.-+. +.+.|++|||...|||..+|++....-.+.|.
T Consensus 237 ~~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 237 QK--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred HH--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 10 11112222221 11 1211 11222211112 36799999999999999999988777766654
No 220
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=88.16 E-value=1.6 Score=34.02 Aligned_cols=39 Identities=31% Similarity=0.388 Sum_probs=29.3
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|.-..||.+-.+ .+++|..|||+.+|++.++|+.++..
T Consensus 9 ~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~~ 47 (61)
T PF12840_consen 9 DPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLKK 47 (61)
T ss_dssp SHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3666667666522 57999999999999999999977643
No 221
>PRK05949 RNA polymerase sigma factor; Validated
Probab=87.81 E-value=4.5 Score=42.48 Aligned_cols=36 Identities=22% Similarity=0.462 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+......+...+|++|+..|+|..+|++.+.+..+
T Consensus 179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~ 214 (327)
T PRK05949 179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREY 214 (327)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 344555667788999999999999999998777654
No 222
>cd00131 PAX Paired Box domain
Probab=87.57 E-value=1.3 Score=40.13 Aligned_cols=42 Identities=17% Similarity=0.022 Sum_probs=31.8
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
|+...|.-|...| .+++|..+||+.||||+.+|..+.++-..
T Consensus 18 lS~d~R~rIv~~~----~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 18 LPDSIRQRIVELA----QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4444444444445 36899999999999999999999988653
No 223
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=87.06 E-value=1.9 Score=34.58 Aligned_cols=42 Identities=21% Similarity=0.198 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 010092 366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNIS-PERYREVMKA 407 (518)
Q Consensus 366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgis-~e~v~~~l~~ 407 (518)
.-.++-....+...+.|..||..|||+.+|++ ...|...|..
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 33445556667778899999999999999997 8888777654
No 224
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=87.01 E-value=13 Score=37.54 Aligned_cols=36 Identities=25% Similarity=0.393 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+......|+..+|++|+..|+|..+|++.+.+..+
T Consensus 119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~ 154 (268)
T PRK06288 119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSL 154 (268)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 445556678889999999999999999998766543
No 225
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=86.80 E-value=5.6 Score=40.08 Aligned_cols=36 Identities=33% Similarity=0.559 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
+......+...+|++|+..|+|..+|++.+.+....
T Consensus 112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~ 147 (257)
T PRK05911 112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF 147 (257)
T ss_pred HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence 344556677889999999999999999987775543
No 226
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=86.79 E-value=1.5 Score=32.71 Aligned_cols=25 Identities=24% Similarity=0.320 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..|+++||+.+|||-.+|..+..+.
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4699999999999999999998764
No 227
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=86.49 E-value=4.3 Score=39.83 Aligned_cols=33 Identities=48% Similarity=0.636 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 236 ~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
...+.+...+|+.|+..|+|..+|++.+.+...
T Consensus 101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~ 133 (231)
T TIGR02885 101 YMKEELSKELGREPTINELAEALGVSPEEIVMA 133 (231)
T ss_pred HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence 445667788999999999999999998776544
No 228
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=86.47 E-value=1.6 Score=35.07 Aligned_cols=24 Identities=21% Similarity=0.230 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+.|..|||+.+|++..+|++++.+
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 599999999999999999866543
No 229
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=86.20 E-value=1.2 Score=34.06 Aligned_cols=42 Identities=29% Similarity=0.352 Sum_probs=31.4
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
|+..|-.||..-+- .++.|..+||+.+++++.+|.++..+-.
T Consensus 1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 46667777766553 4579999999999999999997766543
No 230
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=86.14 E-value=1.4 Score=34.43 Aligned_cols=43 Identities=26% Similarity=0.219 Sum_probs=28.1
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
|+..|..||..-. ....++|..+||+.++++..+|.+.+++-.
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~ 43 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE 43 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5667777776555 235789999999999999999996655543
No 231
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=86.03 E-value=1.6 Score=37.54 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=31.7
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
|++.++.||....- ....|+.+||+.+|+|+.+|++...+-
T Consensus 1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L 41 (108)
T smart00344 1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRL 41 (108)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46677888766442 246999999999999999999776554
No 232
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=85.84 E-value=7.8 Score=39.27 Aligned_cols=36 Identities=33% Similarity=0.478 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
+......+...+|+.|+..|+|..+|++.+.+..++
T Consensus 129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~ 164 (264)
T PRK07122 129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL 164 (264)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 344566777889999999999999999988776543
No 233
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.82 E-value=2.8 Score=38.16 Aligned_cols=51 Identities=25% Similarity=0.270 Sum_probs=38.5
Q ss_pred HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+-.+.-.|++.+-+|+..-. .-..++|..|||+.+|+|+++|. |||++|=
T Consensus 17 dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv~----rsl~~L~ 67 (126)
T COG3355 17 DVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTVY----RSLQNLL 67 (126)
T ss_pred HHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHHH----HHHHHHH
Confidence 455566679999988876544 12468999999999999999997 5666653
No 234
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=85.70 E-value=0.82 Score=44.44 Aligned_cols=40 Identities=23% Similarity=0.114 Sum_probs=29.8
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|+++ +|+.+.- .|..++|.+|||+.||+|+.||+.+...
T Consensus 161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence 35565 5665543 2234799999999999999999998853
No 235
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=85.67 E-value=0.8 Score=34.27 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=19.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHHH
Q 010092 478 TLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 478 Tl~EIA~~LgISrerVRqie~r 499 (518)
|+++||+..|||..+|+..++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 7899999999999999987764
No 236
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=85.62 E-value=6.7 Score=40.91 Aligned_cols=36 Identities=33% Similarity=0.448 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+......+...+|+.|+..|+|..+|++.+.+...
T Consensus 169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~ 204 (317)
T PRK07405 169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY 204 (317)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence 345566677788999999999999999987766543
No 237
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.29 E-value=1.2 Score=41.08 Aligned_cols=37 Identities=16% Similarity=-0.000 Sum_probs=29.2
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+.+.++...+ +++|..|||++||||.++|..+.++.-
T Consensus 10 R~~~~~~~~~-----~G~S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 10 RERVVDAVVG-----EGLSCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred HHHHHHHHHH-----cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence 4444444444 799999999999999999999988754
No 238
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=85.26 E-value=1.1 Score=35.23 Aligned_cols=42 Identities=21% Similarity=0.227 Sum_probs=29.1
Q ss_pred CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 457 L~~rEr~VL~lryGL~-~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
|++....-|...|-|. +++..+..+||+.||+|+.+|....+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 4555555555555443 34679999999999999999985443
No 239
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=85.20 E-value=0.59 Score=37.13 Aligned_cols=41 Identities=32% Similarity=0.303 Sum_probs=30.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|++.|..|+..-. ..++.|..|||+.+|+|+.+|+..+++
T Consensus 5 gLs~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 5 GLSENEAKVYLALL---KNGPATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp CHHHHHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 36777888875432 135899999999999999999865543
No 240
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=85.19 E-value=6.8 Score=37.39 Aligned_cols=62 Identities=11% Similarity=0.160 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhhhccCCCCC---HHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092 283 NLRLVLFVIKKYFQDFANGPR---FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347 (518)
Q Consensus 283 nlrLV~siAkky~~~~~~g~~---~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~ 347 (518)
.+..+..++++|. -.+.. -+|+|.+|.-..++.+..|||++...+-.|.+..+-++..+-|.
T Consensus 46 imkIa~glS~r~n---F~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~ 110 (179)
T PHA02547 46 IMKIAEGLSRRPN---FSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK 110 (179)
T ss_pred HHHHHhccccCCc---cccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence 4445555555554 23444 58999999999999999999999877777666665555554443
No 241
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=84.87 E-value=9.5 Score=38.20 Aligned_cols=35 Identities=29% Similarity=0.434 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
......+..++|++|+.+|+|..+|++.+.+..++
T Consensus 123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~ 157 (254)
T TIGR02850 123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL 157 (254)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34456677889999999999999999988876554
No 242
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=84.82 E-value=10 Score=38.84 Aligned_cols=107 Identities=19% Similarity=0.187 Sum_probs=59.3
Q ss_pred CCCCCHHHHHHHhC--CCHHHHHHHHHhcC--CccccCCCcCCchhhhhcccccCCCCcchhh-hHHHHHHHHHHHHHhc
Q 010092 382 KRVPTDEEIIQGVN--ISPERYREVMKASK--PILSLHSRHGVTQEEFINGITDVDGVENENQ-RQPALLRLALDDVLDS 456 (518)
Q Consensus 382 gR~PT~eELA~~lg--is~e~v~~~l~~~~--~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~-~~~~~l~~~L~~~L~~ 456 (518)
+..+++++||+.++ ||.+++++.+..-. ..+--+..... ......+.......+... -.+.++.+.-.++|+.
T Consensus 135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y--~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~ 212 (271)
T TIGR02147 135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFY--KQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDA 212 (271)
T ss_pred CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcE--EeecceeecCCccchHHHHHHHHHHHHHHHHHHHh
Confidence 44567889999999 99999999887421 22222211000 000011111111112111 1122333444667888
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMV 493 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerV 493 (518)
.|+.+|.+=.+-+|+ ..-++++|.+.+.--+..|
T Consensus 213 ~p~~eR~~S~lT~~i---~~~~~~~i~~~i~~fRk~i 246 (271)
T TIGR02147 213 LPPSERDVSTVTFGI---SEEAYKEIVKKIQEFRKEV 246 (271)
T ss_pred CCccccccceeeEec---CHHHHHHHHHHHHHHHHHH
Confidence 999999998888875 4557777777764433333
No 243
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=84.63 E-value=9.3 Score=39.31 Aligned_cols=35 Identities=34% Similarity=0.641 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
+......+...+|+.|+..|+|..+|++.+.+..+
T Consensus 163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~ 197 (298)
T TIGR02997 163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVREL 197 (298)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 34455667778999999999999999998877654
No 244
>PF12728 HTH_17: Helix-turn-helix domain
Probab=84.63 E-value=1 Score=33.60 Aligned_cols=24 Identities=38% Similarity=0.338 Sum_probs=21.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+|.+|+|+.||||+.+|+++..+.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 589999999999999999998654
No 245
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=84.43 E-value=1.7 Score=35.61 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=35.5
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 447 RLALDDVLDSLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 447 ~~~L~~~L~~L~~rEr~VL~lryG-L~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
...|......|++.|+.|.....- .+....+|..|||+..|||..+|.+..+
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK 56 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence 456777788999999998854331 0112469999999999999999986654
No 246
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=84.26 E-value=2 Score=32.85 Aligned_cols=39 Identities=23% Similarity=0.211 Sum_probs=25.6
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|++-|+.-|-... ..++++.|||..+|-|+..|+..++
T Consensus 4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence 46777777666665 3589999999999999999998753
No 247
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=84.26 E-value=2.3 Score=35.54 Aligned_cols=43 Identities=14% Similarity=0.163 Sum_probs=34.2
Q ss_pred cCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 456 ~L~~rEr~VL~lryG--L~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|+++++.||..--- ...+++-.-++||+.+++|..+||+.+.
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence 388999999876321 2345788999999999999999998764
No 248
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=84.10 E-value=1.2 Score=37.85 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=31.4
Q ss_pred CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
|+|.|..-|..|+-+-. .+++|+.||++.+|+|..+|.+. +++|+.
T Consensus 27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk~ 75 (87)
T PF01371_consen 27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLKY 75 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHHc
Confidence 56666665555542211 25899999999999999999753 445443
No 249
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=84.00 E-value=9.8 Score=39.10 Aligned_cols=25 Identities=28% Similarity=0.262 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 383 RVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 383 R~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
..-|.+|||+.||+|..+|+.++..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4669999999999999999888654
No 250
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=83.82 E-value=2.4 Score=35.94 Aligned_cols=43 Identities=19% Similarity=0.236 Sum_probs=37.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.|+|.-+..|..+.- .++++..++|+.||||+.+++++..|-.
T Consensus 8 ~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 589999988888762 3579999999999999999999988754
No 251
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=83.56 E-value=14 Score=36.01 Aligned_cols=37 Identities=32% Similarity=0.530 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
.+......+...+|++|+..|+|+.+|++.+.+..+.
T Consensus 84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~ 120 (224)
T TIGR02479 84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL 120 (224)
T ss_pred HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4455667788889999999999999999987776543
No 252
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=83.11 E-value=1.6 Score=32.96 Aligned_cols=27 Identities=30% Similarity=0.393 Sum_probs=21.9
Q ss_pred CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 472 DGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 472 ~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
....++|+.|||+.+|+++++|.+++.
T Consensus 14 ~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 14 ESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp CTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334668999999999999999997765
No 253
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=82.99 E-value=2 Score=41.44 Aligned_cols=35 Identities=23% Similarity=0.209 Sum_probs=28.3
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++.|..++. .++|+.+||+.||||++||.++.+.
T Consensus 161 ~~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 161 KEEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred hHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3456666654 5799999999999999999998863
No 254
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=82.88 E-value=1.7 Score=41.00 Aligned_cols=50 Identities=14% Similarity=0.018 Sum_probs=42.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS-----REMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgIS-----rerVRqie~rALkKLR~ 506 (518)
.|+++|.+||.+..- +.+..+|.++|++.++.+ ..+|+.+..+.++||..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 599999999987662 223469999999999986 78999999999999974
No 255
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=82.77 E-value=1.5 Score=31.44 Aligned_cols=25 Identities=28% Similarity=0.244 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.||||+.+|+++.....
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 5889999999999999999988764
No 256
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=82.63 E-value=1.7 Score=40.76 Aligned_cols=50 Identities=22% Similarity=0.154 Sum_probs=41.7
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+||.+.. -+.+..+|.++|++.+. +|..+|+.+..+..+||..
T Consensus 149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~ 203 (219)
T PRK10336 149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS 203 (219)
T ss_pred ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence 49999999998655 12234589999999996 9999999999999999963
No 257
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.56 E-value=17 Score=28.60 Aligned_cols=74 Identities=18% Similarity=0.157 Sum_probs=45.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHH
Q 010092 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESL 463 (518)
Q Consensus 384 ~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~ 463 (518)
++++++||+.+|++...+..++..... .++.+... ...+. .
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~~------------------------~s~~~~~~----~~r~~-----------~ 41 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKETG------------------------TTPKQYLR----DRRLE-----------R 41 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHhC------------------------cCHHHHHH----HHHHH-----------H
Confidence 368899999999999988877653210 01111110 01111 2
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 010092 464 VIRQRFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVKG 500 (518)
Q Consensus 464 VL~lryGL~~~e~~Tl~EIA~~LgI-SrerVRqie~rA 500 (518)
++.+.. ..+.++.+||..+|+ |.....+...+.
T Consensus 42 a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 42 ARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 222222 127899999999999 988887766543
No 258
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=82.40 E-value=1.9 Score=41.43 Aligned_cols=45 Identities=13% Similarity=0.072 Sum_probs=33.8
Q ss_pred hcCCHHHHHHHhHHh--cCCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRF--GLDGKGDRTLGEIAGNLNIS-REMVRKHEVK 499 (518)
Q Consensus 455 ~~L~~rEr~VL~lry--GL~~~e~~Tl~EIA~~LgIS-rerVRqie~r 499 (518)
..|+++|+.||.+-. ...++.+.|..|||+.+|++ +++|+.++.+
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~ 49 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA 49 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence 358999999987744 12234568999999999998 9999865543
No 259
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=82.34 E-value=1.5 Score=31.57 Aligned_cols=24 Identities=29% Similarity=0.339 Sum_probs=21.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+|.+|+|+.||||+.+|+++.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 589999999999999999998765
No 260
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=82.12 E-value=2 Score=40.97 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=43.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+|+.+... +.+...|.++|++.+. +|..+|..+..+.++||..
T Consensus 160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 599999999998763 3345799999999998 9999999999999999974
No 261
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=82.02 E-value=5.3 Score=34.18 Aligned_cols=48 Identities=23% Similarity=0.245 Sum_probs=35.2
Q ss_pred hcCCHHHHHHHhHH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 455 DSLKPKESLVIRQR----FGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 455 ~~L~~rEr~VL~lr----yGL~-~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
..|++++..+|... ||.. .....|..|||+.+|+|+++|+ ++|++|.+
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~ 73 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR 73 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 56899999977632 4422 2357999999999999999988 45555543
No 262
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=81.70 E-value=2.5 Score=31.75 Aligned_cols=29 Identities=31% Similarity=0.440 Sum_probs=22.6
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+... |..|||+.+|+|+.+|++ ++++|.+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~ 46 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVRE----ALSRLEA 46 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 3456 899999999999999985 5555554
No 263
>PRK12423 LexA repressor; Provisional
Probab=81.41 E-value=2.3 Score=41.42 Aligned_cols=48 Identities=27% Similarity=0.350 Sum_probs=33.5
Q ss_pred hcCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010092 455 DSLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 455 ~~L~~rEr~VL~lryG--L~~~e~~Tl~EIA~~Lg-ISrerVRqie~rALkKLR~ 506 (518)
..|++++++|+..--- ..++-.-|..|||+.|| .|+.+|+. +|+.|.+
T Consensus 2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~ 52 (202)
T PRK12423 2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE 52 (202)
T ss_pred CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence 3489999999875321 11223469999999999 59999995 4455544
No 264
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=81.22 E-value=17 Score=36.34 Aligned_cols=37 Identities=22% Similarity=0.250 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
.+.+....+...+|++|+..|+|...|++.+.+..+.
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~ 146 (251)
T PRK07670 110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM 146 (251)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 3444556677889999999999999999988776544
No 265
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=80.93 E-value=2.3 Score=32.90 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=21.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
....|.+|+|+.||||..|||+-+.
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 3578999999999999999997654
No 266
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.82 E-value=3.3 Score=38.34 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=32.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|++.++.||..--- ....|+.+||+.+|+|+.+|+....+
T Consensus 6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 377788888876441 24699999999999999999976654
No 267
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=80.69 E-value=6.6 Score=34.42 Aligned_cols=49 Identities=14% Similarity=0.171 Sum_probs=36.3
Q ss_pred HHHHHHH--hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 448 LALDDVL--DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 448 ~~L~~~L--~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..+...+ ..|++.+..||..-+. .++.|..|||+.+|+++.+|.++..+
T Consensus 15 ~~~~~~l~~~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~ 65 (118)
T TIGR02337 15 SFFRPILAQHGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR 65 (118)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence 3344444 2589999988876552 45799999999999999999755544
No 268
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=80.67 E-value=2.7 Score=39.31 Aligned_cols=50 Identities=14% Similarity=0.094 Sum_probs=41.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+|+.+..- +.+...|.++|++.+. +|..+|..+..+.++||..
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~ 202 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG 202 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence 599999999987651 1124579999999986 9999999999999999964
No 269
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=80.41 E-value=2.4 Score=30.75 Aligned_cols=38 Identities=26% Similarity=0.269 Sum_probs=25.1
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+-|+.+|.-.+- ..+.+..+.|+.||||+.+++..+.+
T Consensus 4 ~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 4 EFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345566555442 23568899999999999999876653
No 270
>PF13551 HTH_29: Winged helix-turn helix
Probab=80.26 E-value=3.1 Score=35.47 Aligned_cols=26 Identities=35% Similarity=0.325 Sum_probs=23.2
Q ss_pred CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDR-TLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~-Tl~EIA~~LgISrerVRqie~rA 500 (518)
++. |..+||+.+|+|+.+|+++.++-
T Consensus 10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 10 EGVSTIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 567 59999999999999999998873
No 271
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=80.23 E-value=1.3 Score=32.29 Aligned_cols=25 Identities=36% Similarity=0.404 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..+|+.++.+.+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988875
No 272
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=79.77 E-value=3.7 Score=29.91 Aligned_cols=25 Identities=28% Similarity=0.391 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+.|..+|++.||+|+.+|++.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999877654
No 273
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=78.92 E-value=3 Score=34.48 Aligned_cols=25 Identities=32% Similarity=0.310 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
..++|..|+|+.||+|+++|+++++
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 4689999999999999999999885
No 274
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=78.81 E-value=3.3 Score=38.90 Aligned_cols=40 Identities=10% Similarity=0.098 Sum_probs=31.2
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
|++.++.||..-- .....|+.|||+.+|+|+.+|++..++
T Consensus 12 lD~~D~~IL~~Lq---~d~R~s~~eiA~~lglS~~tv~~Ri~r 51 (164)
T PRK11169 12 LDRIDRNILNELQ---KDGRISNVELSKRVGLSPTPCLERVRR 51 (164)
T ss_pred HHHHHHHHHHHhc---cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5667788886433 135799999999999999999977655
No 275
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=78.77 E-value=2.1 Score=32.11 Aligned_cols=25 Identities=28% Similarity=0.308 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..|+|+.+|+|+.+|+++++.
T Consensus 8 ~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 8 KGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHhCCCcchhHHHhcC
Confidence 5799999999999999999999876
No 276
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=78.30 E-value=3.3 Score=39.29 Aligned_cols=50 Identities=10% Similarity=0.094 Sum_probs=41.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHH--HHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEI--AGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EI--A~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+||.+..- +.+.-.|.++| |..+++|..+|+.+..+..+||..
T Consensus 156 ~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~ 207 (227)
T TIGR03787 156 DLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQA 207 (227)
T ss_pred cCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhcc
Confidence 499999999987661 11233699999 888999999999999999999974
No 277
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=77.93 E-value=8.4 Score=38.89 Aligned_cols=56 Identities=25% Similarity=0.376 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcC-CC-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 447 RLALDDVLDSLKPKESLVIRQRFGL-DG-KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 447 ~~~L~~~L~~L~~rEr~VL~lryGL-~~-~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+..++-+++.|+=-|.+.+...+-. .+ ..-.+..+||+.+|||+..|+ +|+++|..
T Consensus 167 ka~Vq~Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ir----eAlrkLE~ 224 (251)
T TIGR02787 167 KAAVQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIV----NALRKLES 224 (251)
T ss_pred HHHHHHHHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4467788999998888877765533 33 245899999999999999888 66777754
No 278
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=77.87 E-value=2.9 Score=40.19 Aligned_cols=41 Identities=29% Similarity=0.269 Sum_probs=34.3
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508 (518)
Q Consensus 463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~ 508 (518)
..+.|.- .++|..|||+.||+|++|++-+..|+..+...+.
T Consensus 10 kA~eLk~-----~Glt~gEIAdELNvSreTa~WL~~r~~~~~~~~~ 50 (203)
T COG0856 10 KARELKS-----KGLTTGEIADELNVSRETATWLLTRAFKKESVPA 50 (203)
T ss_pred HHHHHHH-----CCCcHHHhhhhhhhhHHHHHHHHhhhhhccCCCC
Confidence 3455555 6899999999999999999999999988776554
No 279
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.62 E-value=4.6 Score=36.80 Aligned_cols=43 Identities=14% Similarity=0.098 Sum_probs=33.8
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..|++.++.||..--. ....|+.+||+.+|+|..+|+....+-
T Consensus 4 ~~lD~~D~~IL~~L~~---d~r~~~~eia~~lglS~~~v~~Ri~~L 46 (154)
T COG1522 4 MKLDDIDRRILRLLQE---DARISNAELAERVGLSPSTVLRRIKRL 46 (154)
T ss_pred ccccHHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3578888888876431 345999999999999999999876653
No 280
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=77.25 E-value=4 Score=36.80 Aligned_cols=24 Identities=17% Similarity=0.057 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+++|..+||+.||+|+..|+|.++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 589999999999999999999875
No 281
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=76.96 E-value=1.3 Score=35.01 Aligned_cols=25 Identities=36% Similarity=0.420 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
||..|+|+.+|||.++||.++.+.+
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence 4789999999999999999999887
No 282
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=76.90 E-value=4.8 Score=30.50 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=39.4
Q ss_pred cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 456 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e-~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
.+++.+..+|...|..+... .....+||..+|||...|..+...-..+.|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 47888899999988654332 246789999999999999999887766654
No 283
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.71 E-value=3.5 Score=29.65 Aligned_cols=27 Identities=37% Similarity=0.432 Sum_probs=21.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.|..+||+.+|+|+++|++ +++.|.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~----~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSR----TLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 68999999999999999874 4555543
No 284
>PHA01976 helix-turn-helix protein
Probab=76.63 E-value=4.1 Score=31.90 Aligned_cols=26 Identities=8% Similarity=0.179 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|..++|+.+|+|+.+|+++++.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35789999999999999999999864
No 285
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=76.62 E-value=1.7 Score=40.71 Aligned_cols=51 Identities=14% Similarity=0.075 Sum_probs=41.9
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHH-----HHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEI-----AGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EI-----A~~LgISrerVRqie~rALkKLR~~ 507 (518)
.|+++|.+||.+-.- +.+...|.++| |..+++|..+|+.+..+.++||...
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~~ 209 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNPF 209 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhccC
Confidence 599999999988762 12245788888 7789999999999999999999743
No 286
>PRK00215 LexA repressor; Validated
Probab=76.53 E-value=4.3 Score=39.24 Aligned_cols=45 Identities=18% Similarity=0.043 Sum_probs=33.9
Q ss_pred CCHHHHHHHhHHh--cCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRF--GLDGKGDRTLGEIAGNLNI-SREMVRKHEVKGL 501 (518)
Q Consensus 457 L~~rEr~VL~lry--GL~~~e~~Tl~EIA~~LgI-SrerVRqie~rAL 501 (518)
|+++|..||.+-. -...+.+.|+.|||+.+|+ |+++|..++.+-.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 7888999986532 1222457899999999999 9999997766543
No 287
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=76.13 E-value=30 Score=34.61 Aligned_cols=33 Identities=30% Similarity=0.406 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 236 ~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.....+...+|++|+..|+|..+|++.+.+...
T Consensus 127 ~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~ 159 (258)
T PRK08215 127 QVREKLINENSKEPTVEEIAKELEVPREEVVFA 159 (258)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHH
Confidence 445567778999999999999999998887543
No 288
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=76.01 E-value=4.2 Score=31.66 Aligned_cols=37 Identities=22% Similarity=0.234 Sum_probs=27.3
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
|+-.+|.+-+. ...+|+.|||+.+|+|..+|++....
T Consensus 6 rq~~Ll~~L~~---~~~~~~~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK---NKWITLKELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH---HTSBBHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc---CCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 45556665553 46799999999999999999876553
No 289
>PHA00542 putative Cro-like protein
Probab=74.82 E-value=3.9 Score=34.08 Aligned_cols=26 Identities=12% Similarity=0.107 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.++|..++|+.+|||+.+|.++++..
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 57999999999999999999998654
No 290
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=74.77 E-value=4.8 Score=31.12 Aligned_cols=25 Identities=32% Similarity=0.260 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..|||+.+|+|+++|++++++
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5699999999999999999755443
No 291
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=74.73 E-value=8.4 Score=35.69 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=29.4
Q ss_pred HHHHHhcCCHHHHHHHhH----HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 450 LDDVLDSLKPKESLVIRQ----RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 450 L~~~L~~L~~rEr~VL~l----ryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+..+=..|++.|+....+ -|-.++++.+|+.|||+.+|||++++.++.+
T Consensus 4 ~~~le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 4 LKELEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 344446788888873322 1111234679999999999999999999985
No 292
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.51 E-value=3.9 Score=31.97 Aligned_cols=25 Identities=20% Similarity=0.283 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|+|.++|+++++-
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~G 37 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIERG 37 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5789999999999999999999864
No 293
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=74.50 E-value=3.4 Score=30.81 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|+|+++|+++++.
T Consensus 14 ~gltq~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 14 LGLTQADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4789999999999999999999864
No 294
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=74.40 E-value=6.8 Score=31.11 Aligned_cols=25 Identities=24% Similarity=0.242 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
...|..+||+.+|+|+.+|++...+
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 3578999999999999999976655
No 295
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=74.31 E-value=4.9 Score=32.74 Aligned_cols=25 Identities=24% Similarity=0.142 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..|.|+.+|||+.||..+++-
T Consensus 13 ~~ltQ~elA~~vgVsRQTi~~iEkg 37 (68)
T COG1476 13 LGLTQEELAKLVGVSRQTIIAIEKG 37 (68)
T ss_pred hCcCHHHHHHHcCcCHHHHHHHHcC
Confidence 3789999999999999999999864
No 296
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=74.21 E-value=6.6 Score=37.34 Aligned_cols=41 Identities=12% Similarity=0.144 Sum_probs=32.8
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+.-|.-++..|- ++++|++.+|..+|||..|+|++...|..
T Consensus 5 ~e~R~~~R~~YV---~~~~sLe~aA~~~gVs~~TarrWK~~Ak~ 45 (165)
T PF08822_consen 5 QETRDAVRRAYV---FDRLSLEQAAAKCGVSYATARRWKREAKA 45 (165)
T ss_pred HHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344555666663 36899999999999999999999998853
No 297
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=74.16 E-value=6.7 Score=42.28 Aligned_cols=51 Identities=8% Similarity=-0.025 Sum_probs=43.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.+++.||..+.+.+.|...++.|+.++|+.|+||++||.+-+.+.-..|..
T Consensus 10 ~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 10 VLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 478888888777766666678999999999999999999988888777765
No 298
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=73.97 E-value=3.6 Score=32.90 Aligned_cols=27 Identities=44% Similarity=0.455 Sum_probs=21.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++|.++||..+|+|+++|.+ .+++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r----~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSR----ILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHH----HHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence 58999999999999999875 4555553
No 299
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=73.62 E-value=14 Score=33.54 Aligned_cols=48 Identities=13% Similarity=0.049 Sum_probs=36.6
Q ss_pred HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 449 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 449 ~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+...+. .|++.|-.||..-+- .++.|..|||+.+|+++.+|..+..+
T Consensus 28 ~~~~~l~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 28 LLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHHhcccCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444443 489999998886542 35799999999999999999866554
No 300
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=73.56 E-value=81 Score=34.71 Aligned_cols=55 Identities=15% Similarity=0.317 Sum_probs=36.8
Q ss_pred HHHHHHHHH---HHhcCCHHHHHHHhH------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 444 ALLRLALDD---VLDSLKPKESLVIRQ------------RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 444 ~~l~~~L~~---~L~~L~~rEr~VL~l------------ryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
..+.+.+.+ ++..|.-|++.++.. .+|-.--.++++.+||+.+|++.+||++...
T Consensus 283 ~~L~~~lq~A~wLiksL~qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 283 DFLKEKLQEAKWLIKSLEQREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 344555443 356677777766542 2332223579999999999999999997654
No 301
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.35 E-value=9.6 Score=32.39 Aligned_cols=23 Identities=26% Similarity=0.177 Sum_probs=21.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHhc
Q 010092 386 TDEEIIQGVNISPERYREVMKAS 408 (518)
Q Consensus 386 T~eELA~~lgis~e~v~~~l~~~ 408 (518)
|..+||+.+|++...|...++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~ 36 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRY 36 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHH
Confidence 79999999999999999998764
No 302
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=73.12 E-value=6.7 Score=32.89 Aligned_cols=24 Identities=25% Similarity=0.278 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
...|+.+||+.+|||..||+..++
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 468999999999999999998654
No 303
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=73.10 E-value=8.9 Score=37.17 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=35.5
Q ss_pred HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+..|++++..|+.+-.- ..+.|..|||+.+|+|+++|++++.+
T Consensus 137 ~~~~ls~~~~~IL~~l~~---~g~~s~~eia~~l~is~stv~r~L~~ 180 (203)
T TIGR01884 137 LLAGLSREELKVLEVLKA---EGEKSVKNIAKKLGKSLSTISRHLRE 180 (203)
T ss_pred hhcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 345799999999876651 24689999999999999999977665
No 304
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=73.09 E-value=2.1 Score=30.59 Aligned_cols=24 Identities=42% Similarity=0.571 Sum_probs=20.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 478 TLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 478 Tl~EIA~~LgISrerVRqie~rAL 501 (518)
|..|+|+.+|||..++|.++...|
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREGL 24 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTTS
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
Confidence 467999999999999999998763
No 305
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=72.76 E-value=7.3 Score=34.12 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=27.2
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
+.+.|.. .| .+++..++|..+|+|..+|++|+.+....-++.
T Consensus 62 R~~~I~~-~f-----~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 62 RNREIRR-EF-----NGMNVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp HHHHHHH-H-------SS-HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred HHHHHHH-Hh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 5556665 44 378999999999999999999999987776653
No 306
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=72.68 E-value=31 Score=34.34 Aligned_cols=33 Identities=24% Similarity=0.415 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHH
Q 010092 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKK 267 (518)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~ 267 (518)
......++..+|+.|+..|+|..+|++.+.+..
T Consensus 119 ~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~ 151 (255)
T TIGR02941 119 KKAIDELTDHLQRSPKIIEIADHLGLSEEEVLE 151 (255)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence 345567778889999999999999998776644
No 307
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=72.54 E-value=3.9 Score=38.28 Aligned_cols=28 Identities=18% Similarity=0.185 Sum_probs=23.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
++|.+|||..+|+|+++|. |+|++|++.
T Consensus 143 ~~t~~~iA~~lG~tretvs----R~l~~l~~~ 170 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTIT----RLLGDLRKK 170 (193)
T ss_pred CCCHHHHHHHhCCcHHHHH----HHHHHHHHC
Confidence 5899999999999999988 666667653
No 308
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=72.41 E-value=8.2 Score=31.80 Aligned_cols=41 Identities=27% Similarity=0.425 Sum_probs=32.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|+..+..||.+-+. ..++|..+||+.+++|..+|++.+.+
T Consensus 7 ~l~~~~~~il~~l~~---~~~~~~~~la~~~~~s~~~i~~~l~~ 47 (101)
T smart00347 7 GLTPTQFLVLRILYE---EGPLSVSELAKRLGVSPSTVTRVLDR 47 (101)
T ss_pred CCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCchhHHHHHHH
Confidence 477788888877764 24699999999999999998855443
No 309
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.28 E-value=11 Score=32.24 Aligned_cols=54 Identities=24% Similarity=0.249 Sum_probs=35.4
Q ss_pred CCHHHHHH----HhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092 457 LKPKESLV----IRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517 (518)
Q Consensus 457 L~~rEr~V----L~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~ 517 (518)
|++.|+.+ |...|- ...+|.++||..||+|...|..+++-. .++...=.|++|+
T Consensus 3 Ln~eq~~~Tk~elqan~e---l~~LS~~~iA~~Ln~t~~~lekil~~t----qr~~dvW~lRd~l 60 (97)
T COG4367 3 LNPEQKQRTKQELQANFE---LCPLSDEEIATALNWTEVKLEKILQVT----QRPADVWRLRDFL 60 (97)
T ss_pred CCHHHHHHHHHHHHHhhh---hccccHHHHHHHhCCCHHHHHHHHHHh----hccchhHHHHHHH
Confidence 45555444 344553 257999999999999999998877543 3334444566655
No 310
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=72.16 E-value=7.4 Score=29.68 Aligned_cols=26 Identities=35% Similarity=0.477 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|..+||+.+|+|+++|+ +++++|.+
T Consensus 26 ~~~~~la~~~~is~~~v~----~~l~~L~~ 51 (66)
T cd07377 26 PSERELAEELGVSRTTVR----EALRELEA 51 (66)
T ss_pred CCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 459999999999999998 55555654
No 311
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=72.07 E-value=7.2 Score=36.52 Aligned_cols=38 Identities=26% Similarity=0.271 Sum_probs=30.5
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|..-.|=.+|- ..++|..++|+.+|||+.+|.++++.
T Consensus 24 ~p~~~~Ir~~R~----~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 24 TPKEGWVRAIRK----ALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred cCcHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 445444555566 36899999999999999999999984
No 312
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=71.94 E-value=4.7 Score=31.56 Aligned_cols=23 Identities=26% Similarity=0.390 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|..|+|+.+|||..+++.+..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57899999999999999999875
No 313
>PRK13239 alkylmercury lyase; Provisional
Probab=71.70 E-value=7.9 Score=38.14 Aligned_cols=29 Identities=14% Similarity=0.102 Sum_probs=26.7
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 010092 381 LKRVPTDEEIIQGVNISPERYREVMKASK 409 (518)
Q Consensus 381 lgR~PT~eELA~~lgis~e~v~~~l~~~~ 409 (518)
.|++||.++||+.+|++.++++.+|....
T Consensus 33 ~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 33 KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 69999999999999999999999998754
No 314
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=71.56 E-value=11 Score=33.11 Aligned_cols=40 Identities=23% Similarity=0.155 Sum_probs=32.9
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..+.+.+-.-++..+ ++|..++|+.+|+|+.+|+++++..
T Consensus 63 ~~~~~~~i~~~r~~~------gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 63 GLLTPPEIRRIRKKL------GLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred CCcCHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 457887766676666 5799999999999999999998744
No 315
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=71.53 E-value=4.6 Score=38.27 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=28.8
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhC-CCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLN-ISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-ISrerVRqie~r 499 (518)
+..-+.|.-.+ .+++|..|||..|| +|++.|--..+|
T Consensus 5 de~~~~L~~lw----~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLW----AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHH----HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 33444455555 48999999999999 999999988776
No 316
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=71.47 E-value=6.3 Score=39.72 Aligned_cols=51 Identities=16% Similarity=0.131 Sum_probs=40.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 447 RLALDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 447 ~~~L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
...|...+..|++.|+.|..+.. +.. ..+|..|||+..|+|..+|-+.-++
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil--~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kk 57 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVIL--ASPQTAIHSSIATLAKMANVSEPTVNRFCRS 57 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 35678888899999999986543 332 2489999999999999999876554
No 317
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=71.35 E-value=13 Score=31.35 Aligned_cols=32 Identities=19% Similarity=0.031 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010092 475 GDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 475 e~~Tl~EIA~~Lg-ISrerVRqie~rALkKLR~ 506 (518)
-++|+.+||+.|| .+.++|.....+.-++|..
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 4899999999999 9999999888888877765
No 318
>PRK05572 sporulation sigma factor SigF; Validated
Probab=71.28 E-value=44 Score=33.32 Aligned_cols=32 Identities=44% Similarity=0.573 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHH
Q 010092 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVK 266 (518)
Q Consensus 235 ~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~ 266 (518)
......+...+|+.|+..|+|..+|++.+.+.
T Consensus 121 ~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~ 152 (252)
T PRK05572 121 RKDKDELSKELGREPTIEELAEYLGVTPEEVV 152 (252)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHH
Confidence 34455677778999999999999998876653
No 319
>CHL00148 orf27 Ycf27; Reviewed
Probab=71.27 E-value=5.4 Score=37.95 Aligned_cols=50 Identities=16% Similarity=0.094 Sum_probs=42.2
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-------CCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-------NISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-------gISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+|+.+..- +.+.+.|.++|++.+ +++..+|..+..+.++||..
T Consensus 161 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~ 217 (240)
T CHL00148 161 RLTGMEFSLLELLIS-KSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED 217 (240)
T ss_pred EcCHHHHHHHHHHHH-CCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence 499999999987652 223569999999999 48999999999999999975
No 320
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=70.97 E-value=54 Score=34.84 Aligned_cols=36 Identities=39% Similarity=0.600 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.+..++.+|...+|++|+.+|+|..+|++.+.+...
T Consensus 190 kl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m 225 (342)
T COG0568 190 KLRRVKRELLQELGREPTPEEIAEELGVSPDKVREM 225 (342)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHH
Confidence 444566777777999999999999999998765543
No 321
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=70.63 E-value=13 Score=27.86 Aligned_cols=51 Identities=18% Similarity=0.208 Sum_probs=39.9
Q ss_pred cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e-~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.+++.+..+|.-.|..+.+. .....+||..+|+|...|..+......+.+.
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46778888888888654432 2568899999999999999998887776654
No 322
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=70.41 E-value=10 Score=29.05 Aligned_cols=37 Identities=30% Similarity=0.466 Sum_probs=26.3
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..+..|+...+ ..+.+..||++.+|+|..+|+..+.+
T Consensus 7 ~~~~~il~~l~----~~~~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL----EGPLTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH----HCCcCHHHHHHHHCcCHhHHHHHHHH
Confidence 34455555433 12399999999999999999866554
No 323
>PRK10072 putative transcriptional regulator; Provisional
Probab=70.14 E-value=6 Score=34.29 Aligned_cols=25 Identities=24% Similarity=0.355 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|||..+|+++++.
T Consensus 45 ~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 45 TGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5799999999999999999999873
No 324
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=69.78 E-value=4.8 Score=32.23 Aligned_cols=27 Identities=15% Similarity=0.161 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.+.|..+||..+||++++++++.....
T Consensus 22 ~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 22 SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCceEeeecccccccccccHHHHHHh
Confidence 579999999999999999999999886
No 325
>PF14493 HTH_40: Helix-turn-helix domain
Probab=69.78 E-value=11 Score=31.87 Aligned_cols=29 Identities=14% Similarity=0.102 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+++|+.|||+.-|++.+||..++..+...
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 78999999999999999999999998765
No 326
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=69.66 E-value=7.8 Score=39.41 Aligned_cols=53 Identities=26% Similarity=0.229 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+...|...+..|++.|+.|..... ++. ..+|..+||+..|+|..+|-+.-++
T Consensus 14 ~i~~~i~~~~~~Lt~~e~~Ia~yil--~~~~~v~~~si~~lA~~~~vS~aTi~Rf~kk 69 (292)
T PRK11337 14 GLGPYIRMKQEGLTPLESRVVEWLL--KPGDLSEATALKDIAEALAVSEAMIVKVAKK 69 (292)
T ss_pred hHHHHHHHHHhhcCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCChHHHHHHHHH
Confidence 3456788889999999999986543 322 3489999999999999999876543
No 327
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=69.65 E-value=9.3 Score=28.47 Aligned_cols=26 Identities=31% Similarity=0.337 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
++.|..+|++.+|+|+.+|++++++-
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999998777553
No 328
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.33 E-value=10 Score=31.19 Aligned_cols=26 Identities=27% Similarity=0.305 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.+.|..|||+.+|+|+.+|++++..-
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L 44 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTL 44 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47999999999999999999887654
No 329
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=69.31 E-value=55 Score=29.22 Aligned_cols=41 Identities=12% Similarity=-0.040 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 367 ~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
...+.++...+...+...+++++||+.+|+++..+..+.+.
T Consensus 8 ~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 8 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455666667777888899999999999999998877654
No 330
>PRK10870 transcriptional repressor MprA; Provisional
Probab=69.22 E-value=23 Score=33.69 Aligned_cols=52 Identities=10% Similarity=0.017 Sum_probs=37.8
Q ss_pred HHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 448 LALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 448 ~~L~~~L~~--L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..+...|.. |++-+-.||...+. .+..+.|..|||+.+++++.+|.++..+-
T Consensus 42 ~~~~~~l~~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l~l~~~tvsr~v~rL 95 (176)
T PRK10870 42 ENRNKMLKAQGINETLFMALITLES-QENHSIQPSELSCALGSSRTNATRIADEL 95 (176)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344555644 88888888877652 12356899999999999999998666553
No 331
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=69.21 E-value=9.4 Score=31.96 Aligned_cols=30 Identities=27% Similarity=0.257 Sum_probs=24.2
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 473 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 473 ~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++...|-++||+.||+||.+|- +.++.||+
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVw----K~Iq~Lr~ 45 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVW----KHIQQLRE 45 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHH----HHHHHHHH
Confidence 3467999999999999988887 55666774
No 332
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=69.12 E-value=58 Score=32.02 Aligned_cols=33 Identities=42% Similarity=0.656 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268 (518)
Q Consensus 236 ~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~ 268 (518)
.....+...++++|+..|+|..+|++.+.+..+
T Consensus 99 ~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~ 131 (236)
T PRK06986 99 QAIRQLEQELGREPTDTEVAEKLGLSLEEYREM 131 (236)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence 344556678899999999999999998776543
No 333
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=69.01 E-value=6 Score=31.11 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=21.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+|..|+|+.+|||..++|.+..+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g 24 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEF 24 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc
Confidence 578999999999999999998763
No 334
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=68.39 E-value=5 Score=34.04 Aligned_cols=24 Identities=38% Similarity=0.256 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.++|..|||+.+|.|++.|.+++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 368999999999999999998764
No 335
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=68.39 E-value=13 Score=30.97 Aligned_cols=29 Identities=17% Similarity=0.133 Sum_probs=21.7
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHhcC
Q 010092 381 LKRVPTDEEIIQGVNISPERYREVMKASK 409 (518)
Q Consensus 381 lgR~PT~eELA~~lgis~e~v~~~l~~~~ 409 (518)
.|++.|.+.||..+|++.++|..++....
T Consensus 35 ~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 35 KGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp TTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 48999999999999999999999987653
No 336
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=68.39 E-value=64 Score=33.01 Aligned_cols=25 Identities=28% Similarity=0.344 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 383 RVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 383 R~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
..-|..|||+.+|+|.++|+.+...
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~ 271 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKN 271 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 5678999999999999999988654
No 337
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=68.10 E-value=11 Score=33.50 Aligned_cols=28 Identities=7% Similarity=-0.037 Sum_probs=25.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
..++|..+||..+|||..+|+++.....
T Consensus 27 ~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 27 EPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 4689999999999999999999988764
No 338
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=67.05 E-value=10 Score=37.73 Aligned_cols=26 Identities=35% Similarity=0.410 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|..|||++||||..+||+++..
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~ 48 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDD 48 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 35899999999999999999998765
No 339
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=66.79 E-value=18 Score=32.51 Aligned_cols=45 Identities=11% Similarity=0.148 Sum_probs=31.7
Q ss_pred HHHHhcCCHHH-HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 451 DDVLDSLKPKE-SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 451 ~~~L~~L~~rE-r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
..++..|.+.- ..||.+-. +.++++..||++.+|+|+++|++++.
T Consensus 7 ~~~fkaLadptRl~IL~~L~---~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 7 LQLFKILSDETRLGIVLLLR---ESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HHHHHHhCCHHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34555664444 46665433 12579999999999999999998764
No 340
>PRK15482 transcriptional regulator MurR; Provisional
Probab=66.49 E-value=9.6 Score=38.72 Aligned_cols=50 Identities=14% Similarity=0.108 Sum_probs=39.8
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 448 LALDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 448 ~~L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..|......|++.|+.|..... ++. ..+|..|||+..|+|..+|-+.-++
T Consensus 5 ~~i~~~~~~Lt~~e~~Ia~yIl--~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 57 (285)
T PRK15482 5 TKIRNAESEFTENEQKIADFLR--ANVSELKSVSSRKMAKQLGISQSSIVKFAQK 57 (285)
T ss_pred HHHHHHHhhcCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 4677788899999999986543 332 2499999999999999999876554
No 341
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=66.47 E-value=4.4 Score=31.81 Aligned_cols=25 Identities=36% Similarity=0.397 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..+|+.++...+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~~gl 25 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGL 25 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999987665
No 342
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=66.17 E-value=37 Score=38.26 Aligned_cols=103 Identities=15% Similarity=0.123 Sum_probs=58.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHhcCCcc---ccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCH
Q 010092 383 RVPTDEEIIQGVNISPERYREVMKASKPIL---SLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKP 459 (518)
Q Consensus 383 R~PT~eELA~~lgis~e~v~~~l~~~~~~~---SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~ 459 (518)
...|..+||+.+|+|...|+.-+..-...+ .+. ......+ -.+... +. ..+...+..-++
T Consensus 16 ~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~-~i~~~~G---y~l~~~-----~~--------~~~~~~~~~~~~ 78 (584)
T PRK09863 16 QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIG-SISGSAK---YHLEIL-----NR--------RSLFQLLQKSDN 78 (584)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchh-heecCCc---eEEEeC-----CH--------HHHHHHHhcCCH
Confidence 467999999999999998877655321100 000 0000000 000000 00 011122222233
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
|+..+.++..+ .++.++.++|+.|.||++||.+-+.+.-+.|.
T Consensus 79 -e~~~il~~Ll~--~~~~~~~~La~~l~vS~sTi~~dl~~v~~~l~ 121 (584)
T PRK09863 79 -EDRLLLLRLLL--NTFTPMAQLASALNLSRTWVAERLPRLNQRYE 121 (584)
T ss_pred -HHHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHhhh
Confidence 33334444433 35799999999999999999999988887766
No 343
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=66.10 E-value=5.9 Score=31.76 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=19.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|+.|||+.+|||..+|+.+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC
Confidence 3789999999999999998764
No 344
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=66.09 E-value=15 Score=31.91 Aligned_cols=45 Identities=27% Similarity=0.210 Sum_probs=34.4
Q ss_pred cCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL-~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.|++.|-.||..-+-+ ...++.|..+||+.+++++++|.+...+=
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L 67 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL 67 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 5899999988664411 11357999999999999999998766553
No 345
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=65.92 E-value=40 Score=32.74 Aligned_cols=104 Identities=16% Similarity=0.052 Sum_probs=63.0
Q ss_pred HHHHHHHhCCC-CCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHH
Q 010092 374 KLELLFELKRV-PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDD 452 (518)
Q Consensus 374 ~~eL~~elgR~-PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~ 452 (518)
...+..-.|.+ -+.++||+.+|++.+++..++..-.....-+.. + +....-.+ .-......+....+..
T Consensus 9 iEA~LF~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~-g------i~i~~~~~---~y~l~tk~e~~~~v~~ 78 (188)
T PRK00135 9 IEALLFVSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDR-G------LKLIEFND---VYKLVTKEENADYLQK 78 (188)
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCC-C------EEEEEECC---EEEEEEcHHHHHHHHH
Confidence 34455556776 799999999999999998887643221110100 0 00000000 0011122334444554
Q ss_pred HHh-----cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCH
Q 010092 453 VLD-----SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISR 490 (518)
Q Consensus 453 ~L~-----~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISr 490 (518)
+.. .|+.-.-++|...+. .++.|-.||++..|++.
T Consensus 79 ~~~~~~~~~LS~aaLEtLaiIay---~qPiTr~eI~~irGv~~ 118 (188)
T PRK00135 79 LVKTPIKQSLSQAALEVLAIIAY---KQPITRIEIDEIRGVNS 118 (188)
T ss_pred HhcccccCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCH
Confidence 443 599999999888543 57999999999999986
No 346
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=65.79 E-value=7.5 Score=30.73 Aligned_cols=23 Identities=30% Similarity=0.352 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|..|+|+.+|||..++|.++..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 47899999999999999999876
No 347
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=65.34 E-value=12 Score=35.70 Aligned_cols=103 Identities=14% Similarity=0.135 Sum_probs=55.8
Q ss_pred CCCCCHHHHHHHh--CCCHHHHHHHHHhcC--CccccCCCcCCchhhhhcccccCCCCcchhh-hHHHHHHHHHHHHHhc
Q 010092 382 KRVPTDEEIIQGV--NISPERYREVMKASK--PILSLHSRHGVTQEEFINGITDVDGVENENQ-RQPALLRLALDDVLDS 456 (518)
Q Consensus 382 gR~PT~eELA~~l--gis~e~v~~~l~~~~--~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~-~~~~~l~~~L~~~L~~ 456 (518)
+-.+++++||+.+ +||.+++++.+..-. ..+--+.... -......+.......+.-. -.+....+.=.++|+.
T Consensus 37 ~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~--y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al~~ 114 (171)
T PF14394_consen 37 PFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGK--YVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEALDR 114 (171)
T ss_pred CCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCc--EEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 4567899999999 999999999987532 2222121100 0000011111111111111 1122223333466778
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCC
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS 489 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgIS 489 (518)
+|+.+|.+=.+-+|+ ..-++++|.+.+.--
T Consensus 115 ~p~~~R~~s~~T~~v---s~~~~~ki~~~i~~f 144 (171)
T PF14394_consen 115 VPPEERDFSGLTMSV---SREDYEKIKKEIREF 144 (171)
T ss_pred CCccccceeeeEEEe---CHHHHHHHHHHHHHH
Confidence 899999998888875 345666666665333
No 348
>TIGR00647 MG103 conserved hypothetical protein.
Probab=65.24 E-value=13 Score=38.30 Aligned_cols=44 Identities=20% Similarity=0.175 Sum_probs=37.7
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC------CCHHHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN------ISREMVRKHEVKG 500 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg------ISrerVRqie~rA 500 (518)
++.||+..+++..+|.- ..+.|++|+|+.|. ||++.|.....+-
T Consensus 225 l~~Lp~~L~~~a~lRl~---~Pd~SL~ELgell~~~~~~~isKSgvnhRlrKl 274 (279)
T TIGR00647 225 FEKLPLNFQRICLLKID---HPDWSLEQIAEFFASKYKVKISRSGIQHRLRKL 274 (279)
T ss_pred cccCCHHHHHHHHHHHh---CcccCHHHHHHHhccCCCCCcCHHHHHHHHHHH
Confidence 46899999999999883 57899999999994 9999998877664
No 349
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=65.01 E-value=12 Score=32.64 Aligned_cols=45 Identities=29% Similarity=0.431 Sum_probs=33.0
Q ss_pred CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 457 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
|+|.||+-+-.|+-+.. ..++|..||+..||+|..+|- |+=+-|+
T Consensus 38 LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT----RGSN~LK 85 (103)
T COG2973 38 LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT----RGSNSLK 85 (103)
T ss_pred cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc----cchhhhc
Confidence 78888887777664321 247999999999999988774 4545555
No 350
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=64.82 E-value=13 Score=32.69 Aligned_cols=40 Identities=30% Similarity=0.373 Sum_probs=36.0
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
...|++.|-..|+-.+ ++|..+-|..||+|.++|++++..
T Consensus 41 ~~~ls~~eIk~iRe~~------~lSQ~vFA~~L~vs~~Tv~~WEqG 80 (104)
T COG2944 41 VKTLSPTEIKAIREKL------GLSQPVFARYLGVSVSTVRKWEQG 80 (104)
T ss_pred CCCCCHHHHHHHHHHh------CCCHHHHHHHHCCCHHHHHHHHcC
Confidence 3569999999999888 579999999999999999999975
No 351
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=64.18 E-value=8.6 Score=38.77 Aligned_cols=48 Identities=13% Similarity=0.093 Sum_probs=38.1
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 450 LDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 450 L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
|......|++.|+.|..... +.. ..+|..|+|+..|+|..+|-+.-++
T Consensus 3 i~~~~~~Lt~~e~~ia~yil--~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 3 IRQRYPGLAQSDRKLADYLL--LQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hhHhhhhCCHHHHHHHHHHH--hCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 55667889999999986544 322 2499999999999999999877654
No 352
>PHA00738 putative HTH transcription regulator
Probab=63.99 E-value=15 Score=32.65 Aligned_cols=38 Identities=16% Similarity=-0.018 Sum_probs=28.4
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+|.-+.||.+-.. +++++..+|++.|++|+.+|++++.
T Consensus 11 dptRr~IL~lL~~---~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 11 KILRRKILELIAE---NYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred CHHHHHHHHHHHH---cCCccHHHHHHhhCCCHHHHHHHHH
Confidence 3455566654331 3569999999999999999998864
No 353
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=63.94 E-value=8.1 Score=30.21 Aligned_cols=28 Identities=29% Similarity=0.385 Sum_probs=20.5
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092 474 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 474 ~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR 505 (518)
++.+ |..+||+.||||+.+|+ +|+..|.
T Consensus 21 g~~lps~~~la~~~~vsr~tvr----~al~~L~ 49 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVR----EALRRLE 49 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHH----HHHHHHH
T ss_pred CCEeCCHHHHHHHhccCCcHHH----HHHHHHH
Confidence 3567 99999999999999999 4555554
No 354
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=63.66 E-value=16 Score=27.17 Aligned_cols=48 Identities=19% Similarity=0.200 Sum_probs=37.2
Q ss_pred cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e-~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
.+++.+..+|...|..+.+. .....+||..+|+|...|..+......+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 37788888898888654432 2568899999999999999988766544
No 355
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=63.48 E-value=7.2 Score=37.32 Aligned_cols=26 Identities=31% Similarity=0.363 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
-++|..|||+.+|.|..+||++..-.
T Consensus 60 ag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 60 AGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred ccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 37999999999999999999987654
No 356
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=62.78 E-value=2.5 Score=40.98 Aligned_cols=95 Identities=20% Similarity=0.240 Sum_probs=29.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHH
Q 010092 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESL 463 (518)
Q Consensus 384 ~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~ 463 (518)
..+.++||+.++++.+++..++..-+ ++|-. |....+ . ..++.-++...- . ++.-..
T Consensus 52 ~~~~~eia~~l~~~~~~v~~~l~~lQ---~leP~-GigAr~------------l-----~EcLllQl~~~~-~-~~~~~~ 108 (194)
T PF04963_consen 52 TESLEEIAEELGVSEEEVEKALELLQ---SLEPA-GIGARD------------L-----QECLLLQLERKG-P-PDLAYR 108 (194)
T ss_dssp SS-HHHHHHHCTS-HHHHHHHHHHHH---TTSS---TTTS-------------T-----THHHHHHHHHS--S---TTHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH---cCCCC-ccCcCC------------H-----HHHHHHHHhccC-C-cHHHHH
Confidence 35789999999999999999987654 22211 110000 0 112222222111 1 222233
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
||.-++ +......++.||+.+|+|.+.|...... +++|
T Consensus 109 il~~~l--~~l~~~~~~~ia~~l~~s~~~v~~~~~~-Ir~L 146 (194)
T PF04963_consen 109 ILENHL--ELLANKDYKKIAKKLGISEEEVQEAIEL-IRTL 146 (194)
T ss_dssp HHHHHH--HHHHH----------------------------
T ss_pred HHHHHH--HHHHHhhhcccccccccccccccccccc-cccc
Confidence 333333 2223457789999999999999876654 4444
No 357
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=62.55 E-value=13 Score=30.65 Aligned_cols=24 Identities=38% Similarity=0.296 Sum_probs=19.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..|.+|||+.+|+|+..|+++..+
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~ 48 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQK 48 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 489999999999999999977654
No 358
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=62.52 E-value=26 Score=29.23 Aligned_cols=46 Identities=9% Similarity=0.029 Sum_probs=36.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
.|+++++.||-+---.....+-+-+.|-+.||+|.-+-.|.++.-+
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~Li 47 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALI 47 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHh
Confidence 5899999999763222223466889999999999999999998765
No 359
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=62.22 E-value=2e+02 Score=29.82 Aligned_cols=28 Identities=18% Similarity=0.101 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
...|.+|||+..|||..|||+....-..
T Consensus 250 ~~~tq~eva~v~~vtevTIrnrykel~~ 277 (285)
T COG1405 250 ERRTQKEVAKVAGVTEVTIRNRYKELAD 277 (285)
T ss_pred CchHHHHHHHHhCCeeeHHHHHHHHHHH
Confidence 6899999999999999999998854433
No 360
>PRK01905 DNA-binding protein Fis; Provisional
Probab=61.78 E-value=30 Score=28.42 Aligned_cols=37 Identities=19% Similarity=0.189 Sum_probs=25.6
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
-|+.+|...+- ..+-+..+.|+.||||+.+++....+
T Consensus 37 ~E~~~i~~aL~---~~~gn~s~aAr~LGIsrstL~rklkk 73 (77)
T PRK01905 37 VEKPLLEVVME---QAGGNQSLAAEYLGINRNTLRKKLQQ 73 (77)
T ss_pred HHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 35555544331 13457999999999999998877654
No 361
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=61.76 E-value=12 Score=26.74 Aligned_cols=27 Identities=22% Similarity=0.156 Sum_probs=19.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..++|+.+||..+|+|....+++.++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367999999999999988888776554
No 362
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=61.33 E-value=14 Score=36.92 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=32.2
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|+..|+.+-.. ....+..|||+.||||..|||+.+..--.
T Consensus 4 ~R~~~Il~~l~~---~~~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 4 ARQQAIVDLLLN---HTSLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred HHHHHHHHHHHH---cCCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566677665432 35799999999999999999999987544
No 363
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.18 E-value=22 Score=30.47 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=29.6
Q ss_pred HHHHHHHHHhC-CCCCHHHHHHHhCCCHHHHHHHHHhcCC
Q 010092 372 RAKLELLFELK-RVPTDEEIIQGVNISPERYREVMKASKP 410 (518)
Q Consensus 372 ka~~eL~~elg-R~PT~eELA~~lgis~e~v~~~l~~~~~ 410 (518)
....+|+..+. ..-|++|||..||+++.+++.++.+.+.
T Consensus 10 ~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr 49 (97)
T COG4367 10 RTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQR 49 (97)
T ss_pred HHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 34455555544 4458999999999999999999987654
No 364
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=60.67 E-value=10 Score=38.49 Aligned_cols=25 Identities=20% Similarity=0.342 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
++|.+.+||+.||||..+|+.+..|
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr 42 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRR 42 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHh
Confidence 6799999999999999999998875
No 365
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=60.58 E-value=9.3 Score=30.67 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|+|+.+|+++++.
T Consensus 17 ~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 17 LGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999999863
No 366
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=60.46 E-value=13 Score=37.95 Aligned_cols=52 Identities=17% Similarity=0.144 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.+...|....+.|++.|+.|-.+.. .+. ..+|..|||+..|||..+|-+.-+
T Consensus 4 ~l~~~I~~~~~~Lt~~er~iA~yil--~~~~~~~~~si~elA~~a~VS~aTv~Rf~~ 58 (281)
T COG1737 4 NLLERIRERYDSLTKSERKIADYIL--ANPDEVALLSIAELAERAGVSPATVVRFAR 58 (281)
T ss_pred hHHHHHHHHHhcCCHHHHHHHHHHH--hCHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 3556788889999999999986543 322 248999999999999999986544
No 367
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=59.87 E-value=9.3 Score=36.11 Aligned_cols=27 Identities=30% Similarity=0.270 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.|.++||..+|+|+++|. |+|++|++
T Consensus 149 ~~t~~~iA~~lG~tretvs----R~l~~l~~ 175 (202)
T PRK13918 149 YATHDELAAAVGSVRETVT----KVIGELSR 175 (202)
T ss_pred cCCHHHHHHHhCccHHHHH----HHHHHHHH
Confidence 5799999999999999998 55666664
No 368
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=59.31 E-value=8.4 Score=34.27 Aligned_cols=24 Identities=29% Similarity=0.329 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.+.|+.|||+.||||.++|...+.
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRALK 93 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHHH
Confidence 689999999999999999884443
No 369
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=58.75 E-value=9.7 Score=29.41 Aligned_cols=25 Identities=32% Similarity=0.316 Sum_probs=20.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|++++++.++++-
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 5789999999999999999999865
No 370
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=58.69 E-value=13 Score=30.81 Aligned_cols=19 Identities=11% Similarity=0.088 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 010092 478 TLGEIAGNLNISREMVRKH 496 (518)
Q Consensus 478 Tl~EIA~~LgISrerVRqi 496 (518)
+...+|+.||||.+.|+|+
T Consensus 12 s~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW 30 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 7889999999999999998
No 371
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=58.27 E-value=11 Score=31.77 Aligned_cols=42 Identities=19% Similarity=0.279 Sum_probs=27.8
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092 461 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504 (518)
Q Consensus 461 Er~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL 504 (518)
||.|-...|-++ ...|..+.|+.||||.+||.+-...=|.++
T Consensus 6 eR~i~i~~yIi~--~~aTVR~~Ak~FGvSKSTVHkDvteRL~~i 47 (82)
T PF12116_consen 6 ERVIEIANYIIE--TKATVRQAAKVFGVSKSTVHKDVTERLPKI 47 (82)
T ss_dssp HHHHHHHHHHHH--H---HHHHHHHHTS-HHHHHHHHTTHHHHH
T ss_pred HHHHHHHHHHHH--cccHHHHHHHHHCCcHHHHHHHHHHHHHhc
Confidence 445555566553 478999999999999999998776655554
No 372
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=58.25 E-value=9.8 Score=30.35 Aligned_cols=25 Identities=32% Similarity=0.183 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+.|-.|||+.+|+|..+||.++..
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 5799999999999999999988754
No 373
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=58.00 E-value=12 Score=33.23 Aligned_cols=25 Identities=20% Similarity=0.299 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
..+.|..++|..|+||+.+|..+..
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH
Confidence 3678999999999999999999977
No 374
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.93 E-value=27 Score=31.58 Aligned_cols=49 Identities=12% Similarity=0.171 Sum_probs=35.4
Q ss_pred HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 449 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 449 ~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+...+. .|++.+-.||..-+-. .++.|..|||+.+|+++++|.+...+
T Consensus 19 ~~~~~l~~~glt~~q~~vL~~l~~~--~~~~t~~eLa~~l~~~~~tvt~~v~~ 69 (144)
T PRK03573 19 LIDHRLKPLELTQTHWVTLHNIHQL--PPEQSQIQLAKAIGIEQPSLVRTLDQ 69 (144)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHc--CCCCCHHHHHHHhCCChhhHHHHHHH
Confidence 3444443 4899998887765421 24689999999999999999866554
No 375
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=57.55 E-value=18 Score=26.52 Aligned_cols=23 Identities=13% Similarity=0.151 Sum_probs=21.0
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKH 496 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqi 496 (518)
+.+.|+.+||+..|+|+..+.+.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~ 36 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRY 36 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHH
T ss_pred HHhCCHHHHHHHHccchhhHHHH
Confidence 68899999999999999999865
No 376
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=57.40 E-value=6.5 Score=32.57 Aligned_cols=33 Identities=24% Similarity=0.186 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.+..|+.++|+.++||++++.+.....-+.|+.
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467999999999999999999999998888875
No 377
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=57.36 E-value=16 Score=41.79 Aligned_cols=53 Identities=17% Similarity=0.182 Sum_probs=42.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhHHhcCCCC---CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGK---GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~---e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.+.+.|...++.|++.|+.|..+.. .+. ..+|..|||+..|+|..+|-+.-++
T Consensus 342 ~l~~~I~~~~~~Lt~~E~~IA~yIl--~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kk 397 (638)
T PRK14101 342 AVFERIRQMRDALTPAERRVADLAL--NHPRSIINDPIVDIARKADVSQPTVIRFCRS 397 (638)
T ss_pred HHHHHHHHHHhhcCHHHHHHHHHHH--hCHHHHHhccHHHHHHHhCCCHHHHHHHHHH
Confidence 4566788899999999999986543 322 3489999999999999999876554
No 378
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=57.27 E-value=11 Score=36.20 Aligned_cols=29 Identities=41% Similarity=0.508 Sum_probs=24.3
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.+++|+.||++.+|+|+++|++ ++++|..
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~----~lkkL~~ 67 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSM----GLKKLQD 67 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHH----HHHHHHh
Confidence 4799999999999999999985 5666654
No 379
>PRK09726 antitoxin HipB; Provisional
Probab=56.99 E-value=11 Score=31.51 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|||+.+|+++++.
T Consensus 24 ~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 24 NGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4789999999999999999999884
No 380
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=56.76 E-value=14 Score=32.50 Aligned_cols=53 Identities=19% Similarity=0.187 Sum_probs=45.1
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~ 511 (518)
.+|.+-|+....-+| -.-+|-+|||-.++++..+|..+...-..|.|++.+..
T Consensus 27 ~QLkELErvF~ETHY----PDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 27 AQLKELERVFAETHY----PDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHHHHHHHHHhhcC----CcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 357788888888888 45699999999999999999999999999999876543
No 381
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=56.41 E-value=18 Score=30.95 Aligned_cols=44 Identities=25% Similarity=0.209 Sum_probs=30.8
Q ss_pred cCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 456 ~L~~rEr~VL~lryG-L~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.|++.++.||.+.-. -...++.+..+|++.|+++...|++.+..
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~ 88 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDF 88 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHH
Confidence 677888888776544 33457899999999999999999976543
No 382
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=56.40 E-value=12 Score=33.69 Aligned_cols=23 Identities=26% Similarity=0.200 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~r 499 (518)
||-+|+|+.+|+|+.||.++..+
T Consensus 1 MT~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHh
Confidence 68999999999999999998764
No 383
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=56.34 E-value=16 Score=29.11 Aligned_cols=28 Identities=29% Similarity=0.444 Sum_probs=23.1
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+|...|| ...|+|..|++++.+|++...
T Consensus 11 lLi~~~G-------nqtEvaR~l~c~R~TVrKY~~ 38 (64)
T PF06322_consen 11 LLIETYG-------NQTEVARRLGCNRATVRKYSR 38 (64)
T ss_pred HHHHHhC-------cHHHHHHHhcccHHHHHHHhc
Confidence 4556776 688999999999999998753
No 384
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.25 E-value=22 Score=31.45 Aligned_cols=48 Identities=19% Similarity=0.135 Sum_probs=40.4
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.|++.+-+-+.+++- ..=+++||-..+|+|..+||..+...|++|--
T Consensus 40 ~~Lt~d~LeFv~lf~r----~RGnlKEvEr~lg~sYptvR~kld~vlramgy 87 (122)
T COG3877 40 EYLTSDQLEFVELFLR----CRGNLKEVERELGISYPTVRTKLDEVLRAMGY 87 (122)
T ss_pred cccCHhHhHHHHHHHH----HccCHHHHHHHHCCccHHHHHHHHHHHHHcCC
Confidence 5688888888888773 34589999999999999999999999888754
No 385
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=56.08 E-value=8.3 Score=32.97 Aligned_cols=26 Identities=31% Similarity=0.377 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..++|-++...|-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999988653
No 386
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=55.83 E-value=14 Score=25.78 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|+|..+|++++..
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4789999999999999999987753
No 387
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=55.82 E-value=26 Score=34.66 Aligned_cols=36 Identities=25% Similarity=0.391 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
+......+...+|++|+..|+|+.+|++.+.+....
T Consensus 103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~ 138 (231)
T PRK12427 103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL 138 (231)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence 345566788889999999999999999987775543
No 388
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=55.45 E-value=7.8 Score=28.60 Aligned_cols=19 Identities=21% Similarity=0.134 Sum_probs=17.1
Q ss_pred HHHHHhCCCHHHHHHHHHH
Q 010092 481 EIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 481 EIA~~LgISrerVRqie~r 499 (518)
+||+.+|||..+|+++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 7999999999999998764
No 389
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=54.85 E-value=13 Score=36.49 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=22.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.|.++||..+|+|+++|. |++++|++
T Consensus 179 ~lt~~~IA~~lGisretls----R~L~~L~~ 205 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVS----RALSQLQD 205 (230)
T ss_pred cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 5799999999999999988 45566664
No 390
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=54.77 E-value=50 Score=31.97 Aligned_cols=40 Identities=13% Similarity=0.058 Sum_probs=33.4
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|++.|..||..-+. .++.|..+||+.++++.++|.++..
T Consensus 42 gLt~~q~~iL~~L~~---~~~itq~eLa~~l~l~~sTvtr~l~ 81 (185)
T PRK13777 42 DLNINEHHILWIAYH---LKGASISEIAKFGVMHVSTAFNFSK 81 (185)
T ss_pred CCCHHHHHHHHHHHh---CCCcCHHHHHHHHCCCHhhHHHHHH
Confidence 599999999977664 4679999999999999999876544
No 391
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.46 E-value=23 Score=30.02 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=31.9
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
|++.|..||...+-. .+.+..+||+.+++++++|.++..+=
T Consensus 20 lt~~q~~~L~~l~~~---~~~~~~~la~~l~i~~~~vt~~l~~L 60 (126)
T COG1846 20 LTPPQYQVLLALYEA---GGITVKELAERLGLDRSTVTRLLKRL 60 (126)
T ss_pred CCHHHHHHHHHHHHh---CCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 999999999877732 23333999999999999998766553
No 392
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=53.91 E-value=1.1e+02 Score=31.04 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 382 KRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 382 gR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
+..-|..|||+.+|+|...|+.+...
T Consensus 234 ~~~~t~~eIA~~lgvS~~~V~q~~~~ 259 (270)
T TIGR02392 234 DDKLTLQELAAEYGVSAERIRQIEKN 259 (270)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34568999999999999999977643
No 393
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=53.86 E-value=9.2 Score=33.07 Aligned_cols=26 Identities=27% Similarity=0.464 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..++|-++..++-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll 27 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999998764
No 394
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=53.53 E-value=20 Score=31.94 Aligned_cols=26 Identities=19% Similarity=0.125 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
....|..|||+.+|+|+.+|++++..
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 45799999999999999999866543
No 395
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=53.25 E-value=18 Score=35.57 Aligned_cols=29 Identities=17% Similarity=0.231 Sum_probs=24.2
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++.+ |-.++|+.||||+.+|| .||..|..
T Consensus 28 G~~LPsE~eLae~~gVSRt~VR----eAL~~L~~ 57 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLR----EVLQRLAR 57 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 4567 78999999999999999 67777764
No 396
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=53.22 E-value=10 Score=33.16 Aligned_cols=26 Identities=35% Similarity=0.397 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||.+++|-++..+|-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~GLi 26 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLL 26 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 57899999999999999999998754
No 397
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=52.98 E-value=9.8 Score=33.29 Aligned_cols=25 Identities=36% Similarity=0.550 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
||..|+|+.+|||..++|.++...+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999998875
No 398
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=52.95 E-value=10 Score=35.79 Aligned_cols=46 Identities=13% Similarity=-0.034 Sum_probs=38.5
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCC---------HHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRT---------LGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~T---------l~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+||.+-. .+.+ ...||..++++..+|+.+..+..+||..
T Consensus 156 ~Lt~~E~~~l~~l~-----~~~~~v~sr~~l~~~~~~~~~~~~~~tv~~~i~~lr~Kl~~ 210 (232)
T PRK10955 156 ELTGTEFTLLYLLA-----QHLGQVVSREHLSQEVLGKRLTPFDRAIDMHISNLRRKLPD 210 (232)
T ss_pred cCCHHHHHHHHHHH-----hCCCceEcHHHHHHHHhCCCCCCCCcCHHHHHHHHHHhccc
Confidence 59999999998766 3333 4778888999999999999999999974
No 399
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=52.84 E-value=33 Score=25.33 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=17.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|+.+.|+.+||+++|++...+.
T Consensus 17 ~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 17 MSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp S-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHcC
Confidence 99999999999999999966554
No 400
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=52.72 E-value=28 Score=31.71 Aligned_cols=34 Identities=15% Similarity=0.071 Sum_probs=24.7
Q ss_pred HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 462 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 462 r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
+.||.|.. .+.+-.+||..|+||...|++|+.|=
T Consensus 24 ~rIvela~-----~G~rp~~Isr~l~Vs~gcVsKIl~Ry 57 (125)
T PF00292_consen 24 QRIVELAK-----EGVRPCDISRQLRVSHGCVSKILSRY 57 (125)
T ss_dssp HHHHHHHH-----TT--HHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHHhh-----hcCCHHHHHHHHccchhHHHHHHHHH
Confidence 34566666 68999999999999999999998864
No 401
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=52.37 E-value=14 Score=33.43 Aligned_cols=25 Identities=12% Similarity=0.105 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|+.+|||+++|+++++.
T Consensus 17 ~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 17 LKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4789999999999999999999865
No 402
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.16 E-value=14 Score=28.43 Aligned_cols=26 Identities=19% Similarity=0.114 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.++|..++|+..|+|+.+|+++.+.-
T Consensus 9 ~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 9 RGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp TT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 46899999999999999999998854
No 403
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=51.89 E-value=15 Score=35.76 Aligned_cols=27 Identities=22% Similarity=0.397 Sum_probs=22.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+.|.++||..+|+|+++|.++ +++|++
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~----l~~l~~ 210 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRL----LGRFQK 210 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHH----HHHHHH
Confidence 589999999999999999855 556664
No 404
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=51.84 E-value=16 Score=34.74 Aligned_cols=27 Identities=37% Similarity=0.325 Sum_probs=22.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
..|.++||..+|+|+++|++ ++++|++
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR----~l~~l~~ 194 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGR----VLKMLED 194 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHH----HHHHHHH
Confidence 68899999999999999985 5556665
No 405
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=51.72 E-value=11 Score=32.32 Aligned_cols=25 Identities=32% Similarity=0.307 Sum_probs=22.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..++|-++..+|
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gl 25 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGL 25 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 4789999999999999999998875
No 406
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=51.71 E-value=20 Score=28.39 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 010092 478 TLGEIAGNLNISREMVRKH 496 (518)
Q Consensus 478 Tl~EIA~~LgISrerVRqi 496 (518)
+...+|+.||||+.+|+++
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 7889999999999999999
No 407
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=51.62 E-value=22 Score=36.31 Aligned_cols=43 Identities=19% Similarity=0.161 Sum_probs=34.0
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..|++.|+.||.+--+= +...++.||-+.+|+|+.+|++++++
T Consensus 191 ~~L~~~e~~il~~i~~~--GGri~Q~eL~r~lglsktTvsR~L~~ 233 (258)
T COG2512 191 YDLNEDEKEILDLIRER--GGRITQAELRRALGLSKTTVSRILRR 233 (258)
T ss_pred CCCCHHHHHHHHHHHHh--CCEEeHHHHHHhhCCChHHHHHHHHH
Confidence 46999999999875531 23589999999999999999855443
No 408
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.41 E-value=23 Score=35.63 Aligned_cols=38 Identities=18% Similarity=0.209 Sum_probs=28.6
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|...|+.+-- .....+..|+|+.||||..|||+.+..
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TirRdL~~ 42 (251)
T PRK13509 5 QRHQILLELLA---QLGFVTVEKVIERLGISPATARRDINK 42 (251)
T ss_pred HHHHHHHHHHH---HcCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455544422 235799999999999999999999876
No 409
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=51.26 E-value=34 Score=26.44 Aligned_cols=34 Identities=21% Similarity=0.147 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
..+.+..+.|+.|+|.++||+..+.+.-..+--.
T Consensus 10 ~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~d 43 (59)
T PF13556_consen 10 ENNGNISKTARALHIHRNTLRYRLKKIEELLGLD 43 (59)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcC
Confidence 3578999999999999999999999988877543
No 410
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=51.16 E-value=22 Score=35.91 Aligned_cols=41 Identities=17% Similarity=0.294 Sum_probs=30.9
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+|+..|+.+-- .....+..|+|+.||||+.|||+-+.. |.+
T Consensus 5 eR~~~Il~~L~---~~~~v~v~eLa~~l~VS~~TIRRDL~~-Le~ 45 (256)
T PRK10434 5 QRQAAILEYLQ---KQGKTSVEELAQYFDTTGTTIRKDLVI-LEH 45 (256)
T ss_pred HHHHHHHHHHH---HcCCEEHHHHHHHHCCCHHHHHHHHHH-HHH
Confidence 46666665533 124689999999999999999998876 443
No 411
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=51.01 E-value=39 Score=30.62 Aligned_cols=45 Identities=22% Similarity=0.178 Sum_probs=35.0
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh----CCCHHHHHHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL----NISREMVRKHEVKGLMK 503 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L----gISrerVRqie~rALkK 503 (518)
.|++.|..|+....- .++.|..||.+.| +++..||..++.|-.+|
T Consensus 1 ~Lt~~E~~VM~vlW~---~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K 49 (130)
T TIGR02698 1 SISDAEWEVMRVVWT---LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDK 49 (130)
T ss_pred CCCHHHHHHHHHHHc---CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHC
Confidence 478999999877653 3578999977776 79999999888776553
No 412
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=50.96 E-value=11 Score=32.20 Aligned_cols=26 Identities=23% Similarity=0.395 Sum_probs=23.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
|+..|+|+.+|||..++|.++...|-
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~~Gll 26 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLL 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999987753
No 413
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=50.92 E-value=47 Score=33.11 Aligned_cols=56 Identities=25% Similarity=0.332 Sum_probs=43.8
Q ss_pred HHHHHHHhcCCHHHHHHHhHHhc-CCCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092 448 LALDDVLDSLKPKESLVIRQRFG-LDGKGD-RTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507 (518)
Q Consensus 448 ~~L~~~L~~L~~rEr~VL~lryG-L~~~e~-~Tl~EIA~~LgISrerVRqie~rALkKLR~~ 507 (518)
..+.-+++.|+--|.+.+...|+ |||.++ +.-.-||++.||||+ ..-.||+||-..
T Consensus 174 t~V~mAi~tLSYSEleAve~I~eELdG~EG~lvASkiADrvGITRS----VIVNALRKlESA 231 (261)
T COG4465 174 TVVQMAISTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRS----VIVNALRKLESA 231 (261)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHH----HHHHHHHHhhhc
Confidence 34666788999999999998886 455555 788999999999965 445788888653
No 414
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=50.75 E-value=11 Score=31.62 Aligned_cols=25 Identities=32% Similarity=0.422 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..++|.++.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~~Gl 26 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEEKGL 26 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999988775
No 415
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.60 E-value=11 Score=32.51 Aligned_cols=26 Identities=35% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..++|-++...+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~Gll 27 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLI 27 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999987653
No 416
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=50.51 E-value=25 Score=31.95 Aligned_cols=25 Identities=28% Similarity=0.319 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
...+..+||+.||+|..+|+..+.+
T Consensus 21 ~~~~~~ela~~l~vs~~svs~~l~~ 45 (142)
T PRK03902 21 GYARVSDIAEALSVHPSSVTKMVQK 45 (142)
T ss_pred CCcCHHHHHHHhCCChhHHHHHHHH
Confidence 4679999999999999999976544
No 417
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=50.36 E-value=12 Score=32.25 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
++..|+|+.+|||..++|.++...+-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~Gll 26 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLGLI 26 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC
Confidence 47899999999999999999887653
No 418
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.31 E-value=12 Score=32.90 Aligned_cols=26 Identities=31% Similarity=0.460 Sum_probs=23.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..++|-++..++-
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~~gll 26 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLL 26 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999998764
No 419
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.23 E-value=12 Score=32.14 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
|+..|+|+.+|||..+||-++...+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~GL 25 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLREGL 25 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999999876
No 420
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=50.17 E-value=31 Score=33.06 Aligned_cols=39 Identities=13% Similarity=0.100 Sum_probs=28.9
Q ss_pred CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
|++.-|.-|.-.+- ..++|+++||..+||+..||.-|+.
T Consensus 17 lse~~r~~Iy~~~~---~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 17 LSEELREQIYEDVM---QDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCHHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 55555555555553 4577999999999999999976653
No 421
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=50.11 E-value=11 Score=31.63 Aligned_cols=26 Identities=19% Similarity=0.171 Sum_probs=23.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..+|+.++...+-
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~~Gli 27 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLL 27 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 58999999999999999999987654
No 422
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=49.85 E-value=28 Score=32.68 Aligned_cols=43 Identities=23% Similarity=0.203 Sum_probs=29.2
Q ss_pred CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 457 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 457 L~~rEr~VL~lryGL~-~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+++....-|...|-|. +.......+||+.||||+.+|.+.+++
T Consensus 4 ~s~~~edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~r 47 (154)
T COG1321 4 LSETEEDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKR 47 (154)
T ss_pred cchHHHHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHH
Confidence 4444444444444332 345689999999999999999865544
No 423
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=49.80 E-value=19 Score=35.06 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=25.1
Q ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 473 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 473 ~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+.++-.+||+.||||+..|| .||+.|..
T Consensus 31 pG~~L~e~~La~~lgVSRtpVR----EAL~~L~~ 60 (221)
T PRK11414 31 PGARLITKNLAEQLGMSITPVR----EALLRLVS 60 (221)
T ss_pred CCCccCHHHHHHHHCCCchhHH----HHHHHHHH
Confidence 3567889999999999999999 67777764
No 424
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=49.62 E-value=22 Score=34.87 Aligned_cols=30 Identities=17% Similarity=0.205 Sum_probs=25.0
Q ss_pred CCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 473 GKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 473 ~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+.+ |-.++|+.||||+..|| .||.+|..
T Consensus 26 pG~~LpsE~~La~~lgVSRtpVR----EAL~~Le~ 56 (235)
T TIGR02812 26 PGSILPAERELSELIGVTRTTLR----EVLQRLAR 56 (235)
T ss_pred CCCcCcCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence 34668 79999999999999999 67777764
No 425
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.57 E-value=19 Score=31.05 Aligned_cols=23 Identities=26% Similarity=0.440 Sum_probs=21.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|..|+|+.+|||..++|.++..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 57899999999999999999876
No 426
>PRK11050 manganese transport regulator MntR; Provisional
Probab=49.53 E-value=25 Score=32.64 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
++.+..|||+.||+|+++|++.+.+-
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~L 75 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRL 75 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 57899999999999999998665543
No 427
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.30 E-value=12 Score=32.09 Aligned_cols=26 Identities=23% Similarity=0.408 Sum_probs=22.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
++..|+|+.+|||..++|.++...+-
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~~Gll 26 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLV 26 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999887543
No 428
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=49.24 E-value=26 Score=29.12 Aligned_cols=25 Identities=16% Similarity=0.122 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhC------CCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLN------ISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~Lg------ISrerVRqie~r 499 (518)
-++|..++|+.+| +|+.+|.++++-
T Consensus 23 lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 23 LGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred cCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 4789999999999 599999998873
No 429
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.20 E-value=12 Score=32.83 Aligned_cols=26 Identities=31% Similarity=0.479 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
|+..|+|+.+|||..++|-++...|-
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~~GLl 26 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEEQGLL 26 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCC
Confidence 57899999999999999999998753
No 430
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=49.18 E-value=29 Score=33.19 Aligned_cols=44 Identities=23% Similarity=0.213 Sum_probs=32.6
Q ss_pred hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA 500 (518)
..|++-|+.....+. +. ..++|..+||+.+|+|+.+|++.+.-+
T Consensus 101 ~~lt~~e~a~~~~~l-~~-~~g~s~~~iA~~lg~s~~~V~r~l~l~ 144 (187)
T TIGR00180 101 EDLSPIEEAQAYKRL-LE-KFSMTQEDLAKKIGKSRAHITNLLRLL 144 (187)
T ss_pred cCCCHHHHHHHHHHH-HH-HhCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 368888877655443 11 136899999999999999999887543
No 431
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=48.46 E-value=23 Score=35.05 Aligned_cols=38 Identities=21% Similarity=0.317 Sum_probs=28.4
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 463 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 463 ~VL~lryGL~~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+...| ..|+.+ |-.+||+.||||+..|| .||+.|..
T Consensus 19 ~I~~g~l--~pG~~LPsE~eLa~~~gVSRtpVR----EAL~~L~~ 57 (251)
T PRK09990 19 LIVDGVL--KVGQALPSERRLCEKLGFSRSALR----EGLTVLRG 57 (251)
T ss_pred HHHcCCC--CCCCcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3444444 234668 88999999999999999 67777764
No 432
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=48.30 E-value=21 Score=34.35 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
|+.++-.++|+.||||+..|| .||..|..
T Consensus 32 G~~L~e~~La~~lgVSRtpVR----eAL~~L~~ 60 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVR----EAFRALEE 60 (212)
T ss_pred CCEecHHHHHHHhCCChHHHH----HHHHHHHH
Confidence 467899999999999999999 67777764
No 433
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=47.97 E-value=30 Score=24.19 Aligned_cols=25 Identities=28% Similarity=0.314 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..++|..+|+|+.+|.++++.
T Consensus 11 ~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 11 KGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4689999999999999999988764
No 434
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=47.97 E-value=13 Score=31.96 Aligned_cols=25 Identities=28% Similarity=0.317 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..++|.++...+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988775
No 435
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=47.92 E-value=24 Score=34.30 Aligned_cols=39 Identities=15% Similarity=0.242 Sum_probs=28.9
Q ss_pred HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 462 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 462 r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
..|+...| ..|+.++..++|+.||||+..|| .||.+|..
T Consensus 18 ~~I~~g~l--~pG~~L~e~eLae~lgVSRtpVR----EAL~~L~~ 56 (224)
T PRK11534 18 NDIIRGNF--QPDEKLRMSLLTSRYALGVGPLR----EALSQLVA 56 (224)
T ss_pred HHHHhCCC--CCCCcCCHHHHHHHHCCChHHHH----HHHHHHHH
Confidence 34555444 23467899999999999999998 67777754
No 436
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.79 E-value=14 Score=31.44 Aligned_cols=25 Identities=44% Similarity=0.538 Sum_probs=22.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..+|+.+....+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5889999999999999999988765
No 437
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=47.47 E-value=29 Score=30.62 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=26.6
Q ss_pred HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+||.-.|. + .-++|..+.|+.|||++.+|..+.+-
T Consensus 12 EiL~eefl-e-p~glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFL-E-PLGLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHh-c-cccCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45555562 1 12699999999999999999998764
No 438
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=47.31 E-value=23 Score=38.64 Aligned_cols=25 Identities=20% Similarity=0.209 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
-.++|+++||+.+|++.+||++..+
T Consensus 316 LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 316 LKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcCCcHHHHHHHhCCCccchhhhhc
Confidence 4789999999999999999997653
No 439
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=47.29 E-value=13 Score=31.90 Aligned_cols=25 Identities=24% Similarity=0.236 Sum_probs=22.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..++|.++...+
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~~Gl 26 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDRLGL 26 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 6899999999999999999987663
No 440
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.24 E-value=14 Score=32.03 Aligned_cols=26 Identities=31% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
|+..|+|+.+|||..++|-.+...|-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~~GLl 26 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYIDLGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCc
Confidence 57899999999999999999998874
No 441
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.11 E-value=14 Score=32.66 Aligned_cols=27 Identities=30% Similarity=0.461 Sum_probs=24.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
||..|+|+.+|||..++|-++..+|-.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~ 27 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLP 27 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 688999999999999999999987644
No 442
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=47.00 E-value=31 Score=34.47 Aligned_cols=42 Identities=21% Similarity=0.217 Sum_probs=31.6
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.|+..+.+-|++-+-.+ -+.+|...+|+.|+||.+.||+|+.
T Consensus 10 ~Ls~~~~~~ir~L~~~~-p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 10 KLSREAMEQIRYLHKED-PEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCHHHHHHHHHHHHhC-ccccCHHHHHhhCCCCHHHHHHHHh
Confidence 46666666666544322 2458999999999999999999875
No 443
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=46.68 E-value=13 Score=29.66 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
....|+.|||..||+|+++|+..+..
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~ 37 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQ 37 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35789999999999999999987654
No 444
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=46.54 E-value=39 Score=29.96 Aligned_cols=26 Identities=31% Similarity=0.322 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..+.|..|||+.+|+|+..|+++...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 34799999999999999999977654
No 445
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=46.52 E-value=46 Score=31.57 Aligned_cols=53 Identities=28% Similarity=0.289 Sum_probs=33.9
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 450 LDDVLDSLKPKESLVIRQRFGLDGKGD---RTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 450 L~~~L~~L~~rEr~VL~lryGL~~~e~---~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
+...++-+..+.-.||.+...--+..+ +|.++||+.+|+|+.+|. ++++.|.+
T Consensus 46 i~~~l~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~----r~ik~L~e 101 (165)
T PF05732_consen 46 IIKVLDLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVS----RAIKELEE 101 (165)
T ss_pred HHHHhhhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHH----HHHHHHHh
Confidence 344455455555555544331112222 799999999999988877 77777775
No 446
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=46.45 E-value=23 Score=33.54 Aligned_cols=50 Identities=12% Similarity=0.076 Sum_probs=39.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHH-----HHhCCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIA-----GNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA-----~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+||.+.. ...+...|.++|. ..++++..+|+.+..+..+||..
T Consensus 154 ~Lt~~E~~ll~~l~-~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 154 EMGPTEFKLLHFFM-THPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred EcCHHHHHHHHHHH-hCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 59999999997655 2223567877764 46688999999999999999974
No 447
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=46.44 E-value=44 Score=36.58 Aligned_cols=115 Identities=18% Similarity=0.072 Sum_probs=63.2
Q ss_pred hCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHH
Q 010092 381 LKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPK 460 (518)
Q Consensus 381 lgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~r 460 (518)
....-|..+||+.+|+|...++.-+..-...+.-+......... ...+..++ +.. .... ...........
T Consensus 16 ~~~~~~~~~la~~l~vS~Rti~~~i~~In~~l~~~~~~~~~~~~-~~~~~~~~-----~~~---~~~~-~~~~~~~~~~~ 85 (491)
T COG3711 16 KNPLLTIKELAEQLGVSRRTIRYDIKKINESLEEGGIPIIKRKG-GGYILEED-----ERA---LELE-ELQELTSYDKD 85 (491)
T ss_pred hCCCCCHHHHHHHhCccHHHHHHHHHHHHHHHHhCCceEEecCC-CcEEecCc-----HHH---HHHH-hcccccccChH
Confidence 45667889999999999998877665322111100000000000 00011100 000 0000 00001112267
Q ss_pred HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 461 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 461 Er~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
||..+.+-+-+.+ +..++.++|..|++|+.+|.+-.......|..
T Consensus 86 er~~~~ll~~~~~-~~~~l~~La~~l~vs~~ti~~dl~~v~~~l~~ 130 (491)
T COG3711 86 ERIIIILLLLLLS-ELLSLHELADELFVSKSTIINDLKDVRLKLLL 130 (491)
T ss_pred HHHHHHHHHHHhc-ChhhHHHHHHHHHhHHHHHHHHHHHHHHHHHh
Confidence 7777777665544 67999999999999999999999876655553
No 448
>PRK14082 hypothetical protein; Provisional
Probab=46.43 E-value=65 Score=25.99 Aligned_cols=56 Identities=13% Similarity=-0.001 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccch
Q 010092 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332 (518)
Q Consensus 272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFST 332 (518)
+....+.+|..+-+.+.+-... .+-..-+||.||--+.+++.+..++...+.-|-.
T Consensus 7 ~~~e~e~ii~~FepkIkKsL~~-----T~yqeREDLeQElk~Ki~eK~~~~~~~e~PGF~e 62 (65)
T PRK14082 7 DTEEIEHLIENFSPMIKKKLSN-----TSYQEREDLEQELKIKIIEKADMLLCQEVPGFWE 62 (65)
T ss_pred hHHHHHHHHHHccHHHHHHHhc-----CChhhHHHHHHHHHHHHHHHHHHhhcccCCcHHH
Confidence 4556678888888866553322 2345789999999999999999998776554543
No 449
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=46.31 E-value=14 Score=33.07 Aligned_cols=27 Identities=30% Similarity=0.495 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
||..|+|+.+|||..+||-++...|-.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~ 27 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999877654
No 450
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=46.31 E-value=30 Score=30.84 Aligned_cols=33 Identities=33% Similarity=0.280 Sum_probs=24.9
Q ss_pred hHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 466 RQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 466 ~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..+|+ +.....|+.|||+.|.+|+..++.++++
T Consensus 10 ~~~~~-~~~~~vtl~elA~~l~cS~Rn~r~lLkk 42 (115)
T PF12793_consen 10 WQHYG-GQPVEVTLDELAELLFCSRRNARTLLKK 42 (115)
T ss_pred HHHcC-CCCcceeHHHHHHHhCCCHHHHHHHHHH
Confidence 34555 3334689999999999999999877654
No 451
>PRK03837 transcriptional regulator NanR; Provisional
Probab=46.19 E-value=28 Score=34.11 Aligned_cols=29 Identities=24% Similarity=0.325 Sum_probs=24.3
Q ss_pred CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
|+.+ +..++|+.||||+..|| .||..|..
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VR----EAL~~L~~ 63 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVR----EALQALKR 63 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4567 89999999999999999 67777763
No 452
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=46.17 E-value=26 Score=34.79 Aligned_cols=38 Identities=24% Similarity=0.327 Sum_probs=28.1
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 463 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 463 ~VL~lryGL~~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+...| ..|+.+ |-.|+|+.||||+..|| .||+.|..
T Consensus 14 ~I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~Le~ 52 (253)
T PRK10421 14 LIEEKNL--EAGMKLPAERQLAMQLGVSRNSLR----EALAKLVS 52 (253)
T ss_pred HHHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 4454444 234567 68999999999999999 67777764
No 453
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=46.10 E-value=15 Score=32.23 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=23.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..+||.++..+|-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~GLl 26 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLL 26 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 57899999999999999999998754
No 454
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=45.96 E-value=2.3e+02 Score=28.70 Aligned_cols=41 Identities=15% Similarity=0.082 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 367 ~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
...+.++..-+...+...++.++||+.+|+|...+..+.+.
T Consensus 4 ~~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~ 44 (289)
T PRK15121 4 AGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD 44 (289)
T ss_pred HHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44566667777778888999999999999999998887654
No 455
>PRK06424 transcription factor; Provisional
Probab=45.91 E-value=26 Score=32.61 Aligned_cols=25 Identities=8% Similarity=0.094 Sum_probs=23.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|..|+|+.+|+++++|++|++-
T Consensus 96 ~GLSQ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 96 LSMSQADLAAKIFERKNVIASIERG 120 (144)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 5899999999999999999999973
No 456
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=45.91 E-value=31 Score=26.99 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=22.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+.|+.+||+.+|+|...+.++..+..
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 36899999999999999988887654
No 457
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.75 E-value=15 Score=32.55 Aligned_cols=27 Identities=30% Similarity=0.454 Sum_probs=24.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
||..|+|+.+|||..++|-++...|-.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~ 27 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERIGLLP 27 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 588999999999999999999888765
No 458
>PRK10643 DNA-binding transcriptional regulator BasR; Provisional
Probab=45.59 E-value=23 Score=32.91 Aligned_cols=47 Identities=17% Similarity=0.051 Sum_probs=35.3
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCC--HHHHHH-----HhCCCHHHHHHHHHHHHHHHh
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRT--LGEIAG-----NLNISREMVRKHEVKGLMKLK 505 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~T--l~EIA~-----~LgISrerVRqie~rALkKLR 505 (518)
.|+++|.+|+.+..- ..+++ -++|.+ .+++|..+|+.+..+..+||.
T Consensus 149 ~Lt~~E~~il~~l~~---~~g~~~~~~~~~~~~~~~~~~~~~~tv~~~i~~lr~Kl~ 202 (222)
T PRK10643 149 ILTPKEFALLSRLML---KAGSPVHREILYQDIYNWDDEPSSNTLEVHIHNLRDKVG 202 (222)
T ss_pred ecCHHHHHHHHHHHh---CCCceEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhCC
Confidence 599999999986541 23444 444443 368999999999999999996
No 459
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=45.49 E-value=28 Score=31.69 Aligned_cols=29 Identities=17% Similarity=0.218 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++..|..+||+.+|||+..|+ +++.+|++
T Consensus 23 g~~~s~~~ia~~~~is~~~vr----k~l~~L~~ 51 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMV----KIINQLSR 51 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHH----HHHHHHHh
Confidence 346799999999999988888 55566664
No 460
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=45.38 E-value=38 Score=34.06 Aligned_cols=41 Identities=12% Similarity=0.083 Sum_probs=30.5
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+|+..|+.+-- .....+..|+|+.||||.+|||+-+.. |.+
T Consensus 7 eR~~~I~~~l~---~~~~v~v~eLa~~~~VS~~TIRRDL~~-Le~ 47 (252)
T PRK10681 7 ERIGQLLQALK---RSDKLHLKDAAALLGVSEMTIRRDLNA-HSA 47 (252)
T ss_pred HHHHHHHHHHH---HcCCCcHHHHHHHhCCCHHHHHHHHHH-hhc
Confidence 45666655432 135789999999999999999998875 443
No 461
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=45.31 E-value=23 Score=35.78 Aligned_cols=38 Identities=16% Similarity=0.243 Sum_probs=29.7
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.+|.+.|+.+--- ....+.+|+|+.||||..|||+=+.
T Consensus 4 ~eR~~~Il~~l~~---~g~v~v~eLa~~~~VS~~TIRRDL~ 41 (253)
T COG1349 4 EERHQKILELLKE---KGKVSVEELAELFGVSEMTIRRDLN 41 (253)
T ss_pred HHHHHHHHHHHHH---cCcEEHHHHHHHhCCCHHHHHHhHH
Confidence 3577778776441 2468999999999999999998554
No 462
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=44.90 E-value=27 Score=37.58 Aligned_cols=56 Identities=20% Similarity=0.279 Sum_probs=40.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhHHhcCC---C---CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 446 LRLALDDVLDSLKPKESLVIRQRFGLD---G---KGDRTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 446 l~~~L~~~L~~L~~rEr~VL~lryGL~---~---~e~~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+...++.+++.++...+.+...-|+=+ . -..++..|+|+.+|||..+||.++...+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~k~~r~~~i~e~A~~~gvs~~tiR~ye~~gl 64 (388)
T PRK13705 3 LMETLNQCINAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGR 64 (388)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCcCCCccccccCCCCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 345567777777777777666655111 0 1346889999999999999999987765
No 463
>PRK13503 transcriptional activator RhaS; Provisional
Probab=44.87 E-value=1.9e+02 Score=28.68 Aligned_cols=35 Identities=11% Similarity=-0.030 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 373 AKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 373 a~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
...-+........|++++|+.+|+|+..+..+.+.
T Consensus 176 ~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~ 210 (278)
T PRK13503 176 LLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQ 210 (278)
T ss_pred HHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 33334445566789999999999999998877654
No 464
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=44.69 E-value=44 Score=28.68 Aligned_cols=24 Identities=25% Similarity=0.250 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
.++|.++||..||+|.+.|.++++
T Consensus 22 ~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 22 SGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHc
Confidence 579999999999999999998876
No 465
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=44.66 E-value=36 Score=33.80 Aligned_cols=26 Identities=19% Similarity=0.322 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|+.|||+.+|+++++|.+++..
T Consensus 22 ~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 22 RPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 46799999999999999999988764
No 466
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=44.62 E-value=29 Score=34.42 Aligned_cols=39 Identities=18% Similarity=0.317 Sum_probs=28.3
Q ss_pred HHHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 462 SLVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 462 r~VL~lryGL~~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
..|+...| ..|+.+ |-.++|+.||||+..|| .||..|..
T Consensus 21 ~~I~~g~l--~pG~~LpsE~eLa~~lgVSRtpVR----EAL~~L~~ 60 (254)
T PRK09464 21 FLILEGTL--RPGEKLPPERELAKQFDVSRPSLR----EAIQRLEA 60 (254)
T ss_pred HHHHcCCC--CCCCcCCCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 34444444 224566 89999999999999999 67777764
No 467
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=44.48 E-value=33 Score=34.61 Aligned_cols=38 Identities=13% Similarity=0.232 Sum_probs=28.4
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
+|...|+.+-- .....+..|+|+.||||..|||+-+..
T Consensus 5 ~R~~~Il~~l~---~~~~~~~~ela~~l~vS~~TiRRdL~~ 42 (252)
T PRK10906 5 QRHDAIIELVK---QQGYVSTEELVEHFSVSPQTIRRDLND 42 (252)
T ss_pred HHHHHHHHHHH---HcCCEeHHHHHHHhCCCHHHHHHHHHH
Confidence 45666665532 134689999999999999999996544
No 468
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=44.10 E-value=16 Score=32.95 Aligned_cols=26 Identities=38% Similarity=0.515 Sum_probs=23.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+|..|+|+.+|||..++|.++...+-
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~GLl 27 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERHGLI 27 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 68999999999999999999987654
No 469
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=44.07 E-value=51 Score=25.45 Aligned_cols=28 Identities=21% Similarity=0.292 Sum_probs=22.0
Q ss_pred HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092 464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 497 (518)
Q Consensus 464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie 497 (518)
-|..+| .+++.|.|+.|||+...+.++-
T Consensus 9 ~L~~~f------hlp~~eAA~~Lgv~~T~LKr~C 36 (52)
T PF02042_consen 9 DLSQYF------HLPIKEAAKELGVSVTTLKRRC 36 (52)
T ss_pred HHHHHh------CCCHHHHHHHhCCCHHHHHHHH
Confidence 355566 6899999999999987776654
No 470
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=44.05 E-value=30 Score=34.47 Aligned_cols=38 Identities=29% Similarity=0.445 Sum_probs=28.1
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 463 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 463 ~VL~lryGL~~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+...|. .|+.+ |-.++|+.||||+..|| .||..|..
T Consensus 21 ~I~~g~l~--pG~~LpsE~eLa~~~gVSRtpVR----EAL~~L~~ 59 (257)
T PRK10225 21 LIIKTPYN--PGERLPPEREIAEMLDVTRTVVR----EALIMLEI 59 (257)
T ss_pred HHHhCCCC--CCCcCcCHHHHHHHhCCCHHHHH----HHHHHHHH
Confidence 44544442 24567 68899999999999999 67777764
No 471
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=44.01 E-value=30 Score=30.98 Aligned_cols=25 Identities=12% Similarity=0.082 Sum_probs=22.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|.+|+|+.+|||+++|.++++.
T Consensus 17 ~Glsq~eLA~~~Gis~~~is~iE~g 41 (120)
T PRK13890 17 RHMTKKELSERSGVSISFLSDLTTG 41 (120)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 5789999999999999999999864
No 472
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=43.78 E-value=31 Score=25.89 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=19.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKG 500 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rA 500 (518)
.+.+|+++.+|+|+.++.+..+..
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~g 27 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKDG 27 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhcc
Confidence 468999999999999999998754
No 473
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=43.65 E-value=31 Score=32.45 Aligned_cols=26 Identities=15% Similarity=0.239 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|++++|+.+|+|+++|+++++-
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE~G 105 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIENA 105 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 35899999999999999999999963
No 474
>PRK08359 transcription factor; Validated
Probab=43.57 E-value=30 Score=33.36 Aligned_cols=26 Identities=15% Similarity=0.210 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|++|+|+.+|+|+.+|++|++-
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~G 121 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAHG 121 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 35799999999999999999999753
No 475
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=43.54 E-value=3.5e+02 Score=27.06 Aligned_cols=36 Identities=22% Similarity=0.172 Sum_probs=27.9
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 372 ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
++...+...+....+++++|+.+|+|+..+..+.+.
T Consensus 187 ~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~ 222 (290)
T PRK10572 187 EACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQ 222 (290)
T ss_pred HHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 344445556677889999999999999988877654
No 476
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=43.34 E-value=34 Score=38.04 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=32.5
Q ss_pred HHhcCCHHHHHHHhH------------HhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 453 VLDSLKPKESLVIRQ------------RFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 453 ~L~~L~~rEr~VL~l------------ryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
++..|.-|.+.++.. .+|...-.++|+++||+.+|++.+||++..+
T Consensus 334 li~si~qR~~TllkV~~~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 334 LIRNAQQRFDTIQRVAECIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhc
Confidence 345566666666542 2333334789999999999999999997653
No 477
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=43.26 E-value=17 Score=32.27 Aligned_cols=26 Identities=27% Similarity=0.394 Sum_probs=23.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
||..|+|+.+|||..++|-+++..|-
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~GLl 26 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLI 26 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 58899999999999999999988653
No 478
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=43.22 E-value=2.8e+02 Score=28.16 Aligned_cols=32 Identities=41% Similarity=0.601 Sum_probs=25.1
Q ss_pred HHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCL 269 (518)
Q Consensus 238 ~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~ 269 (518)
...+...+|++|+..++|..+|++...+..++
T Consensus 139 ~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~ 170 (285)
T TIGR02394 139 ARQLEKKLGREPSVEEIAELLDKPVEDVSRVL 170 (285)
T ss_pred HHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence 34456678999999999999999987776544
No 479
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.06 E-value=66 Score=30.88 Aligned_cols=39 Identities=31% Similarity=0.263 Sum_probs=27.7
Q ss_pred CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
++....||..-. . ....|-++||..|||+...||+++.+
T Consensus 21 ~~~~~~Vl~~L~--~-~g~~tdeeLA~~Lgi~~~~VRk~L~~ 59 (178)
T PRK06266 21 DEEGFEVLKALI--K-KGEVTDEEIAEQTGIKLNTVRKILYK 59 (178)
T ss_pred CccHhHHHHHHH--H-cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 444455554322 1 24799999999999999999977654
No 480
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=42.70 E-value=2.3e+02 Score=25.53 Aligned_cols=24 Identities=25% Similarity=0.166 Sum_probs=18.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 476 DRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 476 ~~Tl~EIA~~LgISrerVRqie~r 499 (518)
|.|-..||..+|++...|+++...
T Consensus 72 GFsD~~IA~l~~~~e~~vr~~R~~ 95 (123)
T PF02787_consen 72 GFSDRQIARLWGVSEEEVRELRKE 95 (123)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHhccCCCHHHHHHHHHH
Confidence 578899999999999999987654
No 481
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=42.54 E-value=38 Score=32.52 Aligned_cols=37 Identities=14% Similarity=0.072 Sum_probs=27.5
Q ss_pred HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+|++.|+.+-- ..+..+..++|+.||+|.+|||+-+.
T Consensus 7 ~R~~~Il~~l~---~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 7 ERQKALQELIE---ENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHHHH---HCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 45556654432 13568999999999999999998665
No 482
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=42.44 E-value=32 Score=32.65 Aligned_cols=25 Identities=8% Similarity=0.004 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 475 GDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 475 e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
.++|+.++|+.+|+|+++|+++++.
T Consensus 19 ~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 19 QGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4789999999999999999999964
No 483
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=42.38 E-value=38 Score=34.11 Aligned_cols=26 Identities=27% Similarity=0.336 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092 474 KGDRTLGEIAGNLNISREMVRKHEVK 499 (518)
Q Consensus 474 ~e~~Tl~EIA~~LgISrerVRqie~r 499 (518)
..++|+.|||+.+|+++++|.++++.
T Consensus 24 ~~~ls~~eia~~lgl~kstv~RlL~t 49 (263)
T PRK09834 24 DGGATVGLLAELTGLHRTTVRRLLET 49 (263)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34699999999999999999977654
No 484
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=42.20 E-value=41 Score=34.84 Aligned_cols=40 Identities=15% Similarity=-0.001 Sum_probs=30.3
Q ss_pred HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502 (518)
Q Consensus 460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk 502 (518)
+.+.||.+.. .....+..+||+.+|+|+.+|++.+..-..
T Consensus 5 r~~~il~~L~---~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 5 VMLQLLSLLA---DGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHHH---cCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4556665543 135689999999999999999998877554
No 485
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.11 E-value=18 Score=32.16 Aligned_cols=25 Identities=32% Similarity=0.478 Sum_probs=22.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
++..|+|+.+|||..++|-++..+|
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~~GL 25 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYEDKGL 25 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence 5789999999999999999988765
No 486
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=41.99 E-value=54 Score=24.43 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=19.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHh
Q 010092 385 PTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 385 PT~eELA~~lgis~e~v~~~l~~ 407 (518)
-|.+|||+.+|+|...|...+..
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHHHHHH
Confidence 78999999999999999887754
No 487
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=41.71 E-value=52 Score=32.01 Aligned_cols=46 Identities=11% Similarity=-0.023 Sum_probs=30.0
Q ss_pred CCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 457 LKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 457 L~~rEr~VL~lryGL-~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
++.++|.+-.+..-- .+.-+.|.++||..+|+|+++|. |+|++|++
T Consensus 149 ~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs----R~L~~L~~ 195 (226)
T PRK10402 149 FPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL----YVLAQFIQ 195 (226)
T ss_pred ChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH----HHHHHHHH
Confidence 356666654443211 11224689999999999999988 56666665
No 488
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=41.69 E-value=32 Score=37.92 Aligned_cols=45 Identities=18% Similarity=0.373 Sum_probs=31.2
Q ss_pred HhcCCHHHHHHHhH---------Hh---cCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQ---------RF---GLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 454 L~~L~~rEr~VL~l---------ry---GL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
+..|.-|.+.++.. -| |-..-.++|+++||+.+|++.+||++..+
T Consensus 309 i~~i~~R~~TL~~v~~~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 309 IKSLEQRKETLLKVARCIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 44566666655532 22 32224789999999999999999997643
No 489
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=41.61 E-value=37 Score=26.24 Aligned_cols=26 Identities=27% Similarity=0.272 Sum_probs=21.9
Q ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092 382 KRVPTDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 382 gR~PT~eELA~~lgis~e~v~~~l~~ 407 (518)
-|..|..|||+.+|||...+..-++.
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 36778999999999999988777654
No 490
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=41.40 E-value=8.8 Score=36.32 Aligned_cols=47 Identities=17% Similarity=0.146 Sum_probs=0.0
Q ss_pred HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092 450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 498 (518)
Q Consensus 450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~ 498 (518)
|..+...|=..|..-|. .|-..-.++|+++||+.+|++.+||++..+
T Consensus 25 L~~v~~~iv~~Q~~ff~--~g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 25 LLRVAQAIVERQKDFFL--GGPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHh--cCcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 33444445555555443 232234789999999999999999997654
No 491
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=41.35 E-value=48 Score=25.31 Aligned_cols=40 Identities=18% Similarity=0.115 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092 366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVM 405 (518)
Q Consensus 366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l 405 (518)
.+-.+.+....|..+--...+-.+||+.+|+++..|+.-+
T Consensus 10 RL~~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 10 RLPLYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 3333444444554433345788999999999999998643
No 492
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=41.11 E-value=62 Score=29.92 Aligned_cols=46 Identities=17% Similarity=0.168 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCcc
Q 010092 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPIL 412 (518)
Q Consensus 367 ~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~ 412 (518)
-....++..-|...-++..|+.||++.+|++++.|...++..+-.+
T Consensus 29 e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 29 EREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 3344555555666667889999999999999999999988765433
No 493
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=40.82 E-value=29 Score=34.04 Aligned_cols=26 Identities=35% Similarity=0.365 Sum_probs=22.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
-|-.|+|++||||+.||| +||..|..
T Consensus 25 PsE~eLa~~~gVSR~TVR----~Al~~L~~ 50 (233)
T TIGR02404 25 PSEHELMDQYGASRETVR----KALNLLTE 50 (233)
T ss_pred cCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 589999999999999999 67777754
No 494
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=40.42 E-value=37 Score=33.71 Aligned_cols=38 Identities=21% Similarity=0.197 Sum_probs=27.4
Q ss_pred HHHhHHhcCCCCCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092 463 LVIRQRFGLDGKGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 463 ~VL~lryGL~~~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~ 506 (518)
.|+...| ..|+.+ |-.++|+.||||+..|| .||+.|..
T Consensus 20 ~I~~g~l--~pG~~LpsE~eLae~~gVSRtpVR----EAL~~L~~ 58 (253)
T PRK11523 20 RIEQGVY--LVGDKLPAERFIADEKNVSRTVVR----EAIIMLEV 58 (253)
T ss_pred HHHcCCC--CCCCCCCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence 3444444 234567 57899999999999999 67777764
No 495
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=40.41 E-value=21 Score=31.22 Aligned_cols=25 Identities=40% Similarity=0.450 Sum_probs=22.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGL 501 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rAL 501 (518)
+|..|+|+.+|||..++|-++...|
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~~GL 25 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGL 25 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHcCC
Confidence 5789999999999999999998765
No 496
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=40.39 E-value=36 Score=23.59 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHh
Q 010092 386 TDEEIIQGVNISPERYREVMKA 407 (518)
Q Consensus 386 T~eELA~~lgis~e~v~~~l~~ 407 (518)
|-+|||+.+|++.+.|..++..
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHH
Confidence 5579999999999999888754
No 497
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=40.35 E-value=20 Score=32.16 Aligned_cols=27 Identities=30% Similarity=0.466 Sum_probs=23.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092 477 RTLGEIAGNLNISREMVRKHEVKGLMK 503 (518)
Q Consensus 477 ~Tl~EIA~~LgISrerVRqie~rALkK 503 (518)
+|..|+|+.+|||..++|-++...|-.
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~ 27 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLP 27 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 578999999999999999999887653
No 498
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=40.29 E-value=39 Score=31.26 Aligned_cols=50 Identities=14% Similarity=-0.001 Sum_probs=41.1
Q ss_pred cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhC
Q 010092 456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKH 506 (518)
Q Consensus 456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-----gISrerVRqie~rALkKLR~ 506 (518)
.|+++|.+|+.+-.. +.++-.|.++|+..+ ..+..+|..+..+-.+||..
T Consensus 147 ~Lt~~E~~il~~l~~-~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~ 201 (218)
T TIGR01387 147 TLTRKEFQLLWLLMR-RTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDD 201 (218)
T ss_pred eCCHHHHHHHHHHHh-CCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 599999999987762 223458999999998 56778999999999999974
No 499
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.21 E-value=54 Score=34.27 Aligned_cols=43 Identities=26% Similarity=0.208 Sum_probs=35.4
Q ss_pred HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCC--CHHHHHHHHHH
Q 010092 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNI--SREMVRKHEVK 499 (518)
Q Consensus 454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgI--SrerVRqie~r 499 (518)
++.||+..+++-.+|.- .++.|++|||+.+.. |++.|.....|
T Consensus 251 l~~lpe~l~e~a~LRl~---hpd~SLeeLg~~l~~~iSKSGvnHrlrk 295 (308)
T COG1481 251 LEKLPEKLREAALLRLE---HPDASLEELGELLEPPISKSGVNHRLRK 295 (308)
T ss_pred hhhCCHHHHHHHHHhhc---ChhhhHHHHHHHhcCcccHHHHHHHHHH
Confidence 46899999999988873 578999999999987 88887755444
No 500
>PF14747 DUF4473: Domain of unknown function (DUF4473)
Probab=40.17 E-value=2.2e+02 Score=23.71 Aligned_cols=71 Identities=13% Similarity=0.174 Sum_probs=44.0
Q ss_pred CCCHHHHHHHh---CCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh-hhHHHHHHHHHHHHHhcCCH
Q 010092 384 VPTDEEIIQGV---NISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN-QRQPALLRLALDDVLDSLKP 459 (518)
Q Consensus 384 ~PT~eELA~~l---gis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee-~~~~~~l~~~L~~~L~~L~~ 459 (518)
.||.+|+-.+| |||..-+..++.+....-+ ..... ..+.+. .-....+...++..|..+|+
T Consensus 5 ~pt~ee~kaEL~aAGmS~~aidgi~~i~~~~~~--------------~~~~~-~~~~e~~~~~~~~~~~e~~~fikt~s~ 69 (82)
T PF14747_consen 5 PPTEEEAKAELVAAGMSEKAIDGIVKIAEKFKS--------------QFAKA-KGNKEAAKKFFEKYKAEVDAFIKTQSE 69 (82)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHh--------------ccccc-cCCHHHHHHHHHHHHHHHHHHHHHCCH
Confidence 56777776666 9999988888776432111 10000 111111 12334567789999999999
Q ss_pred HHHHHHhHHh
Q 010092 460 KESLVIRQRF 469 (518)
Q Consensus 460 rEr~VL~lry 469 (518)
.++.+..-++
T Consensus 70 ~DQ~~y~~~~ 79 (82)
T PF14747_consen 70 EDQTAYNAFV 79 (82)
T ss_pred HHHHHHHHHH
Confidence 9999886554
Done!